Cayman Islands Species Abundance Analysis
Adam Bruce
09/04/2022
Abstract
QUESTIONS!
How has density index values changed over time on Grand Cayman Island?
How do density index values vary across families of fish?
How do density index values vary across dive sites?
What relationships exist, if any, between these variables and what interpretations can be made from these relationships?
Introduction
Since 1998, Lawrence University Professor Bart De Stasio has led a Marine Term trip to Grand Cayman Island in the Western Caribbean. The objective of this trip has been to document abundance and diversity of fish species, provide evidence towards the health of coral reefs surrounding the island, and to understand the ecological relationships between the fish and coral reef environments. To accomplish this, students on the trip used Reef Environmental Education Foundation (REEF) specification to collect data on 246 fish species at 12 different coral reefs. On each dive, data collection lasted approximately 20 to 50 minutes depending on diver air consumption and non-decompression limits (Timpe, 2018). One of the key variables related to the abundance and diversity of fish was Density Index (Den).
Den was recorded as a measure of how many of a certain species was present at each site during each dive. Ultimately, the scale of Den ranged from 0 to 4, and each whole number represented a REEF category of density. These four categories were Single (S), Few (F), Many (M), and Abundant (A). A Den score of 1 corresponded to S, 2 corresponded to Few, 3 represented Many, and the highest score of 4 was Abundant. Since there were often several dives at a single site, the Den scores for an individual species were averaged to calculate an overall Den for that site each year. REEF provides an outline for performing this calculation and for understanding the specification for each of the four categories. This outline can be seen in the image below.
REEF Density Index Categorization and Average Calculation
As I
proceed, I will perform a statistical analysis, using methods like the
T-Test, to describe important details about similarities and difference
in DENSITY_INDEX for these fish species. Additionally, I will use linear
mixed effect models, since the data is recorded longitudinally, to
investigate both how species density has changed within each dive site
and how species density has changed between the dive sites. Finally, I
will build a machine learning model to best predict a fish species based
on OOBE/RMSE comparison metrics. This will allow future researchers to
understand under what conditions they may expect to find a certain reef
species. Collectively, these results will help explain the ecology of
coral reef fish species on Grand Cayman Island.
Initial Data Wrangling
Initially, data consisted of 246 rows and 95 columns. However, the
data set was not in tidy form as information on one variable, Density
Index, was spread across many columns. These columns were also labeled
by year and location, which meant they needed to be separated into
individual variables. To tidy the data, I used the concepts of pivoting
and separating. First, I made the Density Index variable (DENSITY_INDEX)
using the pivot_longer function. This function condensed
the columns into one hence making the data set “longer”. Next, I used
the seperate function to make individual variable columns
for the location and year each observation was collected. Finally, YEAR
was coded as a character variable and I changed it to numeric. After
this, the data set consisted of 22,632 rows and 5 columns. However, some
of the Density Index values followed an outdated version of the REEF
scale. So, values greater than the 4.0 threshold were removed.
## # A tibble: 6 x 6
## SPECIES_NAME FISH_ID YEAR LOCATION DENSITY_INDEX DEPTH
## <chr> <dbl> <dbl> <chr> <dbl> <chr>
## 1 Blue Angelfish 1 1998 CH 0 Shallow
## 2 Blue Angelfish 1 1998 DG 2 Deep
## 3 Blue Angelfish 1 1998 SB 0 Deep
## 4 Blue Angelfish 1 1998 SC 0 Deep
## 5 Blue Angelfish 1 1998 TF 0 Deep
## 6 Blue Angelfish 1 2000 CP 0 DeepThe head function shows that the five variables consist
of two character variables in SPECIES_NAME and LOCATION, and three
numeric variables in FISH_ID, YEAR, and DENSITY_INDEX. Overall, 12
locations were studied throughout the duration of data collection. These
sites include, from southeast clockwise to northeast, Bodden Bay Lagoon
(BL), Beach Bay (BB), Smith’s Cove (SC), Sunset House (SH), Sea View
(SV), Casuarina Point (CP), Devil’s Grotto (DG), Eden’s Rock (ER),
Cemetery Reef (CR), Turtle Farm (TF), Spanish Bay (SB), and Mangroves
(MG). A majority of these sites were described and shown geographically
in 2018 by Alec Timpe, a Marine Term student of Professor De Stasio. His
dive site image and site description paper can be seen below. 
Right click to copy the link, then paste into a web browser: Timpe_Description
Exploratory Analysis
## # A tibble: 6 x 3
## SPECIES_NAME MEAN_DEN STD_DENSITY
## <chr> <dbl> <dbl>
## 1 Fairy Basslet 2.67 0.437
## 2 Blue Tang 1.83 1.30
## 3 Threespot Damselfish 1.82 0.804
## 4 Rock Beauty 1.79 0.532
## 5 Spotfin Butterflyfish 1.71 0.755
## 6 Blue Chromis 1.69 1.70| Species Name | Mean Density | Variance |
|---|---|---|
| Fairy Basslet | 2.672946 | 0.4366565 |
| Blue Tang | 1.825481 | 1.2962784 |
| Threespot Damselfish | 1.818636 | 0.8040828 |
| Rock Beauty | 1.788302 | 0.5317684 |
| Spotfin Butterflyfish | 1.714757 | 0.7551484 |
| Blue Chromis | 1.693575 | 1.7015532 |
| Species Name | Mean Density | Variance |
|---|---|---|
| Belted Sandfish | 0 | 0 |
| Black Jack | 0 | 0 |
| Creole-fish | 0 | 0 |
| Mottled Mojarra | 0 | 0 |
| Orangesided Goby | 0 | 0 |
| Palometa | 0 | 0 |
REEF Fish Density Index at Twelve Sampling Locations on Grand Cayman Island
Biyearly Mean REEF Fish Density Index Scores on Grand Cayman Island
## # A tibble: 22,543 x 6
## SPECIES_NAME FISH_ID LOCATION DENSITY_INDEX DEPTH YEAR1998
## <chr> <dbl> <chr> <dbl> <chr> <dbl>
## 1 Blue Angelfish 1 CH 0 Shallow 0
## 2 Blue Angelfish 1 DG 2 Deep 0
## 3 Blue Angelfish 1 SB 0 Deep 0
## 4 Blue Angelfish 1 SC 0 Deep 0
## 5 Blue Angelfish 1 TF 0 Deep 0
## 6 Blue Angelfish 1 CP 0 Deep 2
## 7 Blue Angelfish 1 DG 0 Deep 2
## 8 Blue Angelfish 1 SC 0 Deep 2
## 9 Blue Angelfish 1 CH 0 Shallow 2
## 10 Blue Angelfish 1 SB 0 Deep 2
## # … with 22,533 more rows
## # A tibble: 6 x 4
## SPECIES_NAME MEAN_DI SD_SPECIES N
## <chr> <dbl> <dbl> <int>
## 1 Fairy Basslet 2.67 0.437 90
## 2 Blue Tang 1.83 1.30 90
## 3 Threespot Damselfish 1.82 0.804 91
## 4 Rock Beauty 1.79 0.532 92
## 5 Spotfin Butterflyfish 1.71 0.755 91
## 6 Blue Chromis 1.69 1.70 91| Species Name | Mean Density Index | Standard Deviation | Sample Size |
|---|---|---|---|
| Fairy Basslet | 2.672946 | 0.4366565 | 90 |
| Blue Tang | 1.825481 | 1.2962784 | 90 |
| Threespot Damselfish | 1.818636 | 0.8040828 | 91 |
| Rock Beauty | 1.788302 | 0.5317684 | 92 |
| Spotfin Butterflyfish | 1.714757 | 0.7551484 | 91 |
| Blue Chromis | 1.693575 | 1.7015532 | 91 |
## # A tibble: 6 x 2
## SPECIES_NAME MEAN
## <chr> <dbl>
## 1 Fairy Basslet 2.67
## 2 Blue Tang 1.83
## 3 Threespot Damselfish 1.82
## 4 Rock Beauty 1.79
## 5 Spotfin Butterflyfish 1.71
## 6 Blue Chromis 1.69## # A tibble: 15 x 2
## SPECIES_NAME MEAN
## <chr> <dbl>
## 1 Belted Sandfish 0
## 2 Black Jack 0
## 3 Creole-fish 0
## 4 Mottled Mojarra 0
## 5 Orangesided Goby 0
## 6 Palometa 0
## 7 Peppermint Bass 0
## 8 Reef Croaker 0
## 9 Roughhead Blenny 0
## 10 Round Scad 0
## 11 Sand Perch 0
## 12 Sheepshead 0
## 13 Silver Porgy 0
## 14 Spiny Blenny 0
## 15 Sponge Cardinalfish 0
To Do
MIXTURE MODEL PROBABILISTIC MODEL OF SUBPOPULATIONS WITHIN AN OVERALL POPULATION.
MCLUS Package: Nothing to do with the Biological aspect just based on abundance.
Two Part
Statistical Analysis on Entire Dataset
## [1] 1.747203## [1] 1.715242##
## BB CH CP CR DG
## 0 0.0653642065 0.0390738061 0.0897250362 0.0610226725 0.0979257115
## 1 0.0036179450 0.0036179450 0.0084418717 0.0050651230 0.0089242644
## 2 0.0028943560 0.0014471780 0.0077182827 0.0079594790 0.0108538350
## 3 0.0009647853 0.0007235890 0.0024119633 0.0016883743 0.0021707670
##
## ER HM SB SC SH
## 0 0.0246020260 0.0180897250 0.0909310178 0.1025084419 0.0658465991
## 1 0.0031355523 0.0012059817 0.0065123010 0.0074770863 0.0045827303
## 2 0.0024119633 0.0016883743 0.0110950314 0.0079594790 0.0055475157
## 3 0.0004823927 0.0004823927 0.0028943560 0.0026531597 0.0021707670
##
## SV TF
## 0 0.0906898215 0.0851423058
## 1 0.0084418717 0.0062711047
## 2 0.0103714424 0.0106126387
## 3 0.0026531597 0.0019295707##
## Pearson's Chi-squared test
##
## data: Compare_Locations
## X-squared = 35.731, df = 33, p-value = 0.3413## # A tibble: 12 x 7
## LOCATION MEAN ST.DEV ST.ERR N upper.95 lower.95
## <chr> <dbl> <dbl> <dbl> <int> <dbl> <dbl>
## 1 BB 0.411 0.840 0.0203 1718 0.451 0.372
## 2 CH 0.379 0.828 0.0265 979 0.431 0.327
## 3 CP 0.443 0.859 0.0173 2454 0.477 0.409
## 4 CR 0.499 0.883 0.0213 1719 0.541 0.458
## 5 DG 0.462 0.886 0.0170 2701 0.496 0.429
## 6 ER 0.520 0.923 0.0341 733 0.587 0.453
## 7 HM 0.402 0.826 0.0373 491 0.475 0.329
## 8 SB 0.446 0.868 0.0176 2429 0.480 0.411
## 9 SC 0.342 0.773 0.0149 2698 0.371 0.313
## 10 SH 0.424 0.851 0.0205 1716 0.464 0.384
## 11 SV 0.483 0.888 0.0179 2453 0.518 0.448
## 12 TF 0.486 0.894 0.0180 2452 0.522 0.451
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 11 6.6317 3.504e-11 ***
## 22531
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Shapiro-Wilk normality test
##
## data: CAYMAN_SUBSET
## W = 0.56506, p-value < 2.2e-16## # A tibble: 22,543 x 6
## SPECIES_NAME FISH_ID YEAR LOCATION DENSITY_INDEX DEPTH
## <chr> <dbl> <dbl> <chr> <dbl> <chr>
## 1 Blue Angelfish 1 1998 CH 0 Shallow
## 2 Blue Angelfish 1 1998 DG 1.10 Deep
## 3 Blue Angelfish 1 1998 SB 0 Deep
## 4 Blue Angelfish 1 1998 SC 0 Deep
## 5 Blue Angelfish 1 1998 TF 0 Deep
## 6 Blue Angelfish 1 2000 CP 0 Deep
## 7 Blue Angelfish 1 2000 DG 0 Deep
## 8 Blue Angelfish 1 2000 SC 0 Deep
## 9 Blue Angelfish 1 2000 CH 0 Shallow
## 10 Blue Angelfish 1 2000 SB 0 Deep
## # … with 22,533 more rows## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 11 7.2889 1.442e-12 ***
## 22531
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Shapiro-Wilk normality test
##
## data: CAYMAN_LOG_SUBSET
## W = 0.57299, p-value < 2.2e-16
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 11 6.6317 3.504e-11 ***
## 22531
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Shapiro-Wilk normality test
##
## data: CAYMAN_SQRT_SUBSET
## W = 0.56607, p-value < 2.2e-16
##
## Kruskal-Wallis rank sum test
##
## data: DENSITY_INDEX by LOCATION
## Kruskal-Wallis chi-squared = 84.794, df = 11, p-value = 1.733e-13
GROUPING FISH BY FAMILY
Stats On New Family Variable
##
## Apogonidae Carangidae Gobiidae Haemulidae Holocentridae
## BB 0.0018631061 0.0037262121 0.0055893182 0.0049682828 0.0018631061
## CH 0.0010646320 0.0021292641 0.0031495364 0.0028390188 0.0010646320
## CP 0.0026615801 0.0053231602 0.0079403806 0.0070975469 0.0026615801
## CR 0.0018631061 0.0037262121 0.0055893182 0.0049682828 0.0018631061
## DG 0.0029277381 0.0058554762 0.0087832143 0.0078073016 0.0028833784
## ER 0.0007984740 0.0015969481 0.0023510624 0.0021292641 0.0007541144
## HM 0.0005323160 0.0010646320 0.0015525884 0.0014195094 0.0005323160
## SB 0.0026615801 0.0052788005 0.0079847403 0.0070531872 0.0025285011
## SC 0.0029277381 0.0058554762 0.0087832143 0.0078073016 0.0028833784
## SH 0.0018631061 0.0037262121 0.0055893182 0.0049682828 0.0018187464
## SV 0.0026615801 0.0053231602 0.0079847403 0.0070088276 0.0026615801
## TF 0.0026615801 0.0053231602 0.0079403806 0.0070975469 0.0026615801
##
## Labridae Lutjanidae Other Pomacentridae Scaridae
## BB 0.0046577652 0.0031051768 0.0306525307 0.0042585281 0.0040367298
## CH 0.0026615801 0.0017743867 0.0174777093 0.0023954221 0.0023067027
## CP 0.0066095906 0.0044359668 0.0438273522 0.0061659939 0.0057223972
## CR 0.0046577652 0.0031051768 0.0306525307 0.0043028878 0.0040367298
## DG 0.0072749856 0.0048795635 0.0482633190 0.0067426696 0.0063434326
## ER 0.0019961851 0.0013307900 0.0130417424 0.0018631061 0.0017300271
## HM 0.0013307900 0.0008871934 0.0087832143 0.0012420707 0.0011533514
## SB 0.0065652309 0.0043028878 0.0434724748 0.0059441955 0.0056336779
## SC 0.0072306259 0.0048795635 0.0481745997 0.0067426696 0.0063434326
## SH 0.0046577652 0.0030608171 0.0306081711 0.0043028878 0.0040367298
## SV 0.0066539502 0.0044359668 0.0437386328 0.0061659939 0.0057667569
## TF 0.0066539502 0.0044359668 0.0437386328 0.0060772745 0.0057667569
##
## Serranidae Sparidae
## BB 0.0093155303 0.0021736237
## CH 0.0053231602 0.0012420707
## CP 0.0133079005 0.0031051768
## CR 0.0093155303 0.0021736237
## DG 0.0146386905 0.0034156945
## ER 0.0039923701 0.0009315530
## HM 0.0026615801 0.0006210354
## SB 0.0132191811 0.0031051768
## SC 0.0146386905 0.0034156945
## SH 0.0093155303 0.0021736237
## SV 0.0133079005 0.0031051768
## TF 0.0133079005 0.0031051768## # A tibble: 12 x 7
## SCIENTIFIC_FAMILY MEAN ST.DEV ST.ERR N upper.95 lower.95
## <chr> <dbl> <dbl> <dbl> <int> <dbl> <dbl>
## 1 Apogonidae 0.205 0.628 0.0267 552 0.258 0.153
## 2 Carangidae 0.181 0.594 0.0179 1103 0.216 0.146
## 3 Gobiidae 0.178 0.608 0.0150 1651 0.207 0.149
## 4 Haemulidae 0.322 0.767 0.0200 1469 0.361 0.283
## 5 Holocentridae 1.14 1.17 0.0500 545 1.23 1.04
## 6 Labridae 0.470 0.860 0.0232 1374 0.515 0.424
## 7 Lutjanidae 0.568 0.904 0.0299 916 0.627 0.510
## 8 Other 0.417 0.816 0.00857 9072 0.434 0.400
## 9 Pomacentridae 1.17 1.27 0.0356 1267 1.24 1.10
## 10 Scaridae 0.706 1.02 0.0295 1192 0.763 0.648
## 11 Serranidae 0.299 0.648 0.0123 2758 0.323 0.275
## 12 Sparidae 0.247 0.706 0.0278 644 0.302 0.193
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 11 188.13 < 2.2e-16 ***
## 22531
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Kruskal-Wallis rank sum test
##
## data: DENSITY_INDEX by SCIENTIFIC_FAMILY
## Kruskal-Wallis chi-squared = 1553.1, df = 11, p-value < 2.2e-16
### Graphical Visualization by Families
| Scientific Family | Mean Density Index | Standard Deviation | Standard Error | Sample Size | Upper 95% CI | Lower 95% CI |
|---|---|---|---|---|---|---|
| Pomacentridae | 1.1735051 | 1.2654297 | 0.0355508 | 1267 | 1.2431834 | 1.1038267 |
| Holocentridae | 1.1365635 | 1.1671619 | 0.0499957 | 545 | 1.2345533 | 1.0385737 |
| Scaridae | 0.7055519 | 1.0169367 | 0.0294548 | 1192 | 0.7632822 | 0.6478216 |
| Lutjanidae | 0.5683379 | 0.9041616 | 0.0298743 | 916 | 0.6268906 | 0.5097853 |
| Labridae | 0.4696159 | 0.8600878 | 0.0232033 | 1374 | 0.5150935 | 0.4241383 |
| Other | 0.4168636 | 0.8162553 | 0.0085699 | 9072 | 0.4336602 | 0.4000669 |
| Haemulidae | 0.3222590 | 0.7671973 | 0.0200169 | 1469 | 0.3614914 | 0.2830267 |
| Serranidae | 0.2990534 | 0.6480974 | 0.0123408 | 2758 | 0.3232409 | 0.2748659 |
| Sparidae | 0.2472986 | 0.7055934 | 0.0278043 | 644 | 0.3017940 | 0.1928033 |
| Apogonidae | 0.2052027 | 0.6280289 | 0.0267307 | 552 | 0.2575939 | 0.1528115 |
| Carangidae | 0.1812783 | 0.5939445 | 0.0178837 | 1103 | 0.2163298 | 0.1462269 |
| Gobiidae | 0.1778428 | 0.6081996 | 0.0149683 | 1651 | 0.2071802 | 0.1485055 |
Modeling
TWO PART MODEL: A Specialized Mixture Model
why?
A two-part model is a flexible statistical model specifically designed to deal with limited dependent variables. The distinguishing feature of these variables is that the range of values they may assume has a lower bound occurring in a fair number of observations.
How?
The zeros are typically handled using a model for the probability of a positive outcome:
φ(y > 0) = Pr(y > 0|x) = F(xδ)
where x is a vector of explanatory variables, δ is the corresponding vector of parameters to be estimated, and F is the cumulative distribution function of an independent and identically distributed error term, typically chosen to be from extreme value (logit) or normal (probit) distributions
For the positives, the model is usually represented as:
φ(y|y > 0, x) = g(xγ)
where x is a vector of explanatory variables, γ is the corresponding vector of parameters to be estimated, and g is an appropriate density function for y|y > 0
TWO PART MODEL OKAY?
DISCRETE_CONTINUOUS MORE_DIS_CON
## # A tibble: 1 x 2
## NUMBER_ZEROS NUMBER_NONZEROS
## <int> <int>
## 1 17230 5313
## # A tibble: 6 x 7
## SPECIES_NAME FISH_ID YEAR LOCATION DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## <chr> <dbl> <dbl> <chr> <dbl> <chr> <chr>
## 1 Blue Angelfish 1 1998 CH 0 Shallow Other
## 2 Blue Angelfish 1 1998 DG 1 Deep Other
## 3 Blue Angelfish 1 1998 SB 0 Deep Other
## 4 Blue Angelfish 1 1998 SC 0 Deep Other
## 5 Blue Angelfish 1 1998 TF 0 Deep Other
## 6 Blue Angelfish 1 2000 CP 0 Deep Other## SPECIES_NAME FISH_ID YEAR LOCATION
## Length:22543 Min. : 1.0 Min. :1998 Length:22543
## Class :character 1st Qu.: 62.0 1st Qu.:2004 Class :character
## Mode :character Median :124.0 Median :2010 Mode :character
## Mean :123.5 Mean :2009
## 3rd Qu.:185.0 3rd Qu.:2014
## Max. :246.0 Max. :2018
## DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## Min. :0.0000 Length:22543 Length:22543
## 1st Qu.:0.0000 Class :character Class :character
## Median :0.0000 Mode :character Mode :character
## Mean :0.2357
## 3rd Qu.:0.0000
## Max. :1.0000## SPECIES_NAME FISH_ID YEAR LOCATION
## Length:22543 Min. : 1.0 Min. :1998 Length:22543
## Class :character 1st Qu.: 62.0 1st Qu.:2004 Class :character
## Mode :character Median :124.0 Median :2010 Mode :character
## Mean :123.5 Mean :2009
## 3rd Qu.:185.0 3rd Qu.:2014
## Max. :246.0 Max. :2018
## DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## Min. :0.0000 Length:22543 Length:22543
## 1st Qu.:0.0000 Class :character Class :character
## Median :0.0000 Mode :character Mode :character
## Mean :0.2357
## 3rd Qu.:0.0000
## Max. :1.0000
##
## Call:
## lm(formula = DENSITY_INDEX ~ YEAR + LOCATION + SCIENTIFIC_FAMILY,
## data = CAYMAN_NO_ZEROS)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.48441 -0.53776 0.02514 0.39531 2.12473
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 18.746855 2.978887 6.293 3.36e-10 ***
## YEAR -0.008330 0.001482 -5.619 2.02e-08 ***
## LOCATIONCH 0.006098 0.056702 0.108 0.91437
## LOCATIONCP -0.050214 0.042300 -1.187 0.23525
## LOCATIONCR -0.068164 0.044375 -1.536 0.12457
## LOCATIONDG -0.005260 0.041457 -0.127 0.89905
## LOCATIONER 0.047679 0.056643 0.842 0.39997
## LOCATIONHM -0.041584 0.070504 -0.590 0.55534
## LOCATIONSB -0.008841 0.042516 -0.208 0.83528
## LOCATIONSC -0.078548 0.043704 -1.797 0.07235 .
## LOCATIONSH 0.005918 0.046569 0.127 0.89888
## LOCATIONSV -0.018147 0.041701 -0.435 0.66345
## LOCATIONTF -0.009118 0.041709 -0.219 0.82695
## SCIENTIFIC_FAMILYCarangidae -0.068427 0.104937 -0.652 0.51438
## SCIENTIFIC_FAMILYGobiidae 0.100639 0.099986 1.007 0.31421
## SCIENTIFIC_FAMILYHaemulidae -0.051533 0.093722 -0.550 0.58245
## SCIENTIFIC_FAMILYHolocentridae 0.238211 0.092645 2.571 0.01016 *
## SCIENTIFIC_FAMILYLabridae -0.205604 0.090808 -2.264 0.02360 *
## SCIENTIFIC_FAMILYLutjanidae -0.153563 0.092485 -1.660 0.09689 .
## SCIENTIFIC_FAMILYOther -0.229688 0.085542 -2.685 0.00727 **
## SCIENTIFIC_FAMILYPomacentridae 0.373821 0.088163 4.240 2.27e-05 ***
## SCIENTIFIC_FAMILYScaridae 0.009882 0.089947 0.110 0.91252
## SCIENTIFIC_FAMILYSerranidae -0.461519 0.088767 -5.199 2.08e-07 ***
## SCIENTIFIC_FAMILYSparidae 0.071857 0.111073 0.647 0.51770
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.6371 on 5289 degrees of freedom
## Multiple R-squared: 0.1293, Adjusted R-squared: 0.1255
## F-statistic: 34.16 on 23 and 5289 DF, p-value: < 2.2e-16Consider Predicting on next few years… Time Series Analysis.
K MEANS AND HIERARCHICAL CLUSTERING
## 14111328 dissimilarities, summarized :
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.0000 0.4692 0.6289 0.6019 0.6692 1.0000
## Metric : mixed ; Types = N, N, I, N, N
## Number of objects : 5313## # A tibble: 2 x 5
## YEAR LOCATION DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## <fct> <fct> <dbl> <fct> <fct>
## 1 2008 SC 2.9 Deep Holocentridae
## 2 2008 SC 2.89 Deep Holocentridae## # A tibble: 2 x 5
## YEAR LOCATION DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## <fct> <fct> <dbl> <fct> <fct>
## 1 2018 SC 3.88 Deep Pomacentridae
## 2 1998 CH 1 Shallow Other
## [[1]]
## YEAR LOCATION DENSITY_INDEX DEPTH
## 2018 :261 DG :403 Min. :1.000 Deep :539
## 1998 : 65 CR : 43 1st Qu.:1.667 Shallow: 0
## 2002 : 50 SV : 40 Median :2.000
## 2004 : 37 SH : 39 Mean :1.967
## 2000 : 34 CP : 14 3rd Qu.:2.183
## 2006 : 34 BB : 0 Max. :3.500
## (Other): 58 (Other): 0
## SCIENTIFIC_FAMILY cluster
## Other :262 Min. :1
## Scaridae : 48 1st Qu.:1
## Serranidae : 38 Median :1
## Lutjanidae : 32 Mean :1
## Haemulidae : 29 3rd Qu.:1
## Holocentridae: 29 Max. :1
## (Other) :101
##
## [[2]]
## YEAR LOCATION DENSITY_INDEX DEPTH
## 2012 :319 SV :386 Min. :1.000 Deep :641
## 2002 : 76 SH : 65 1st Qu.:1.000 Shallow: 0
## 2000 : 41 CP : 52 Median :1.667
## 2010 : 39 TF : 46 Mean :1.745
## 2006 : 38 CR : 23 3rd Qu.:2.000
## 2004 : 35 BB : 20 Max. :3.500
## (Other): 93 (Other): 49
## SCIENTIFIC_FAMILY cluster
## Other :353 Min. :2
## Labridae : 45 1st Qu.:2
## Lutjanidae : 42 Median :2
## Scaridae : 42 Mean :2
## Holocentridae: 36 3rd Qu.:2
## Pomacentridae: 33 Max. :2
## (Other) : 90
##
## [[3]]
## YEAR LOCATION DENSITY_INDEX DEPTH
## 2008 :292 SC :378 Min. :1.000 Deep :671
## 2010 : 66 CP : 59 1st Qu.:1.600 Shallow: 0
## 2006 : 58 CR : 49 Median :2.000
## 2002 : 47 SH : 48 Mean :1.930
## 2000 : 43 DG : 40 3rd Qu.:2.200
## 2014 : 43 BB : 37 Max. :3.667
## (Other):122 (Other): 60
## SCIENTIFIC_FAMILY cluster
## Other :346 Min. :3
## Labridae : 51 1st Qu.:3
## Scaridae : 47 Median :3
## Pomacentridae: 39 Mean :3
## Holocentridae: 38 3rd Qu.:3
## Haemulidae : 33 Max. :3
## (Other) :117
##
## [[4]]
## YEAR LOCATION DENSITY_INDEX DEPTH
## 2014 :333 BB :233 Min. :1.000 Deep :507
## 2002 : 47 SH : 51 1st Qu.:1.800 Shallow: 0
## 2004 : 37 CP : 49 Median :2.000
## 2018 : 34 TF : 47 Mean :2.011
## 2012 : 33 CR : 45 3rd Qu.:2.333
## 2000 : 23 DG : 45 Max. :3.857
## (Other): 0 (Other): 37
## SCIENTIFIC_FAMILY cluster
## Other :228 Min. :4
## Scaridae : 66 1st Qu.:4
## Pomacentridae: 42 Median :4
## Labridae : 37 Mean :4
## Lutjanidae : 29 3rd Qu.:4
## Holocentridae: 26 Max. :4
## (Other) : 79
##
## [[5]]
## YEAR LOCATION DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## 2018 :330 TF :407 Min. :1.000 Deep :652 Other :394
## 2000 : 53 CP : 58 1st Qu.:1.000 Shallow: 0 Scaridae : 54
## 2006 : 51 SH : 45 Median :1.250 Serranidae: 43
## 1998 : 49 SC : 41 Mean :1.475 Labridae : 36
## 2002 : 45 SB : 37 3rd Qu.:2.000 Lutjanidae: 29
## 2016 : 41 CR : 31 Max. :3.500 Haemulidae: 23
## (Other): 83 (Other): 33 (Other) : 73
## cluster
## Min. :5
## 1st Qu.:5
## Median :5
## Mean :5
## 3rd Qu.:5
## Max. :5
##
##
## [[6]]
## YEAR LOCATION DENSITY_INDEX DEPTH
## 2010 :429 SB :433 Min. :1.000 Deep :727
## 2014 : 63 DG : 70 1st Qu.:1.500 Shallow: 63
## 1998 : 53 HM : 63 Median :2.000
## 2006 : 53 CR : 61 Mean :1.934
## 2018 : 44 SH : 52 3rd Qu.:2.200
## 2000 : 42 CP : 43 Max. :3.667
## (Other):106 (Other): 68
## SCIENTIFIC_FAMILY cluster
## Other :361 Min. :6
## Labridae : 59 1st Qu.:6
## Holocentridae: 55 Median :6
## Pomacentridae: 55 Mean :6
## Scaridae : 53 3rd Qu.:6
## Lutjanidae : 49 Max. :6
## (Other) :158
##
## [[7]]
## YEAR LOCATION DENSITY_INDEX DEPTH
## 2018 :108 ER :198 Min. :1.000 Deep : 0
## 2012 : 61 BB : 0 1st Qu.:1.271 Shallow:198
## 2016 : 29 CH : 0 Median :2.000
## 1998 : 0 CP : 0 Mean :1.915
## 2000 : 0 CR : 0 3rd Qu.:2.333
## 2002 : 0 DG : 0 Max. :3.667
## (Other): 0 (Other): 0
## SCIENTIFIC_FAMILY cluster
## Other :82 Min. :7
## Pomacentridae:25 1st Qu.:7
## Scaridae :17 Median :7
## Serranidae :17 Mean :7
## Holocentridae:12 3rd Qu.:7
## Labridae :12 Max. :7
## (Other) :33
##
## [[8]]
## YEAR LOCATION DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## 2014 :77 CH :193 Min. :1.000 Deep : 0 Other :89
## 1998 :49 HM : 31 1st Qu.:1.333 Shallow:224 Pomacentridae:30
## 2000 :37 BB : 0 Median :2.000 Serranidae :26
## 2004 :31 CP : 0 Mean :1.939 Scaridae :18
## 2016 :30 CR : 0 3rd Qu.:2.425 Labridae :17
## 2002 : 0 DG : 0 Max. :3.889 Lutjanidae :13
## (Other): 0 (Other): 0 (Other) :31
## cluster
## Min. :8
## 1st Qu.:8
## Median :8
## Mean :8
## 3rd Qu.:8
## Max. :8
##
##
## [[9]]
## YEAR LOCATION DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## 2012 :176 CR :183 Min. :1.000 Deep :448 Serranidae:273
## 2010 : 55 CP : 46 1st Qu.:1.000 Shallow: 9 Labridae : 41
## 2006 : 53 SH : 40 Median :1.000 Scaridae : 29
## 2018 : 44 SB : 37 Mean :1.302 Other : 26
## 2014 : 31 DG : 34 3rd Qu.:1.500 Haemulidae: 20
## 2008 : 29 BB : 32 Max. :3.286 Lutjanidae: 20
## (Other): 69 (Other): 85 (Other) : 48
## cluster
## Min. :9
## 1st Qu.:9
## Median :9
## Mean :9
## 3rd Qu.:9
## Max. :9
##
##
## [[10]]
## YEAR LOCATION DENSITY_INDEX DEPTH
## 2018 :242 CP :268 Min. :1.000 Deep :630
## 2002 : 54 SV : 55 1st Qu.:2.000 Shallow: 4
## 2000 : 53 DG : 48 Median :2.500
## 2014 : 46 SB : 48 Mean :2.471
## 2006 : 45 TF : 47 3rd Qu.:3.000
## 2012 : 43 SH : 46 Max. :3.875
## (Other):151 (Other):122
## SCIENTIFIC_FAMILY cluster
## Pomacentridae:362 Min. :10
## Scaridae : 49 1st Qu.:10
## Holocentridae: 37 Median :10
## Labridae : 36 Mean :10
## Haemulidae : 28 3rd Qu.:10
## Lutjanidae : 27 Max. :10
## (Other) : 95## # A tibble: 10 x 5
## YEAR LOCATION DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## <fct> <fct> <dbl> <fct> <fct>
## 1 2018 DG 2 Deep Other
## 2 2012 SV 1.67 Deep Other
## 3 2008 SC 2 Deep Other
## 4 2014 BB 2 Deep Other
## 5 2018 TF 1.25 Deep Other
## 6 2010 SB 2 Deep Other
## 7 2018 ER 2 Shallow Other
## 8 2014 CH 2 Shallow Other
## 9 2012 CR 1 Deep Serranidae
## 10 2018 CP 2.43 Deep Pomacentridae
## [[1]]
## YEAR LOCATION DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## 2018 :986 DG :581 Min. :1.000 Deep :2049 Other :1137
## 2010 :261 CP :256 1st Qu.:1.600 Shallow: 221 Serranidae: 205
## 2008 :146 SB :245 Median :2.000 Scaridae : 194
## 2002 :138 SC :228 Mean :1.912 Labridae : 126
## 2006 :137 CR :207 3rd Qu.:2.000 Lutjanidae: 118
## 2004 :133 SH :164 Max. :3.750 Haemulidae: 114
## (Other):469 (Other):589 (Other) : 376
## cluster
## Min. :1
## 1st Qu.:1
## Median :1
## Mean :1
## 3rd Qu.:1
## Max. :1
##
##
## [[2]]
## YEAR LOCATION DENSITY_INDEX DEPTH
## 2012 :620 SV :500 Min. :1.000 Deep :1577
## 2010 :247 CP :189 1st Qu.:1.000 Shallow: 145
## 2008 :155 SB :185 Median :1.250
## 2014 :121 CR :172 Mean :1.489
## 2002 :115 SC :147 3rd Qu.:2.000
## 2006 :103 SH :130 Max. :3.500
## (Other):361 (Other):399
## SCIENTIFIC_FAMILY cluster
## Other :910 Min. :2
## Serranidae :239 1st Qu.:2
## Labridae :137 Median :2
## Scaridae :100 Mean :2
## Lutjanidae : 86 3rd Qu.:2
## Holocentridae: 72 Max. :2
## (Other) :178
##
## [[3]]
## YEAR LOCATION DENSITY_INDEX DEPTH
## 2014 :444 TF :370 Min. :1.000 Deep :1189
## 2010 :134 CP :144 1st Qu.:2.000 Shallow: 132
## 2000 :115 SB :142 Median :2.333
## 2008 : 98 SC :125 Mean :2.313
## 2006 : 92 BB : 99 3rd Qu.:2.833
## 1998 : 85 CR : 97 Max. :3.889
## (Other):353 (Other):344
## SCIENTIFIC_FAMILY cluster
## Pomacentridae:534 Min. :3
## Scaridae :129 1st Qu.:3
## Other :114 Median :3
## Holocentridae:101 Mean :3
## Labridae :100 3rd Qu.:3
## Serranidae : 99 Max. :3
## (Other) :244## # A tibble: 3 x 5
## YEAR LOCATION DENSITY_INDEX DEPTH SCIENTIFIC_FAMILY
## <fct> <fct> <dbl> <fct> <fct>
## 1 2018 DG 2 Deep Other
## 2 2012 SV 1.25 Deep Other
## 3 2014 TF 2.38 Deep Pomacentridae
Truncated Model?
1998 K-MEANS
## K-means clustering with 4 clusters of sizes 3, 197, 45, 1
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 3.3708185 -5.838370
## 2 -0.4338479 0.121128
## 3 1.6524260 0.121128
## 4 0.9964154 -11.797868
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 2 2
## Atlantic Spadefish Balloonfish
## 2 2
## Banded Butterflyfish Bandtail Puffer
## 3 2
## Bar Jack Barred Cardinalfish
## 2 2
## Barred Hamlet Beaugregory
## 3 2
## Belted Cardinalfish Belted Sandfish
## 2 2
## Bicolor Damselfish Black Durgon
## 3 3
## Black Grouper Black Hamlet
## 3 2
## Black Jack Blackbar Soldierfish
## 2 2
## Blackcap Basslet Blackear Wrasse
## 2 2
## Blackfin Snapper Blue Angelfish
## 2 2
## Blue Chromis Blue Goby
## 1 2
## Blue Hamlet Blue Parrotfish
## 2 2
## Blue Runner Blue Tang
## 2 3
## Bluehead Bluelip Parrotfish
## 3 2
## Bluespotted Cornetfish Bluestriped Grunt
## 2 3
## Boga Bonefish
## 2 2
## Bonnetmouth Bridled Goby
## 2 2
## Brown Chromis Brown Garden Eel
## 3 4
## Bucktooth Parrotfish Butter Hamlet
## 2 2
## Caesar Grunt Cero
## 2 2
## Chain Moray Chalk Bass
## 2 2
## Cherubfish Chub (Bermuda/Yellow)
## 2 2
## Cleaning Goby Clown Wrasse
## 2 2
## Cocoa Damselfish Colon Goby
## 2 2
## Common Snook Coney
## 2 2
## Cottonwick Creole Wrasse
## 2 3
## Creole-fish Crevalle Jack
## 2 2
## Cubbyu Cubera Snapper
## 2 2
## Darkheaded Blenny Diamond Blenny
## 2 2
## Doctorfish Dog Snapper
## 3 2
## Dusky Damselfish Dusky Squirrelfish
## 3 2
## Eyed Flounder Fairy Basslet
## 2 1
## Flamefish Flying Gurnard
## 2 2
## Foureye Butterflyfish French Angelfish
## 3 3
## French Grunt Gag
## 3 2
## Glasseye Snapper Glassy Sweeper
## 2 2
## Goldentail Moray Goldspot Goby
## 2 2
## Goliath Grouper (Jewfish) Gray Angelfish
## 2 2
## Gray Snapper Gray Triggerfish
## 2 2
## Graysby Great Barracuda
## 3 3
## Greater Amberjack Greater Soapfish
## 2 2
## Green Moray Green Razorfish
## 2 2
## Green Sea Turtle Greenblotch Parrotfish
## 2 2
## Hairy Blenny Harlequin Bass
## 2 3
## Hawksbill Sea Turtle Highhat
## 2 2
## Hogfish Honeycomb Cowfish
## 2 2
## Horse-eye Jack Houndfish
## 2 2
## Hovering Goby Hybrid Hamlet
## 2 2
## Indigo Hamlet Jackknife Fish
## 2 2
## Jolthead Porgy Lancer Dragonet
## 2 2
## Lane Snapper Lantern Bass
## 2 2
## Lionfish Loggerhead Sea Turtle
## 2 2
## Longfin Damselfish Longjaw Squirrelfish
## 2 2
## Longsnout Butterflyfish Longspine Squirrelfish
## 2 2
## Mahogany Snapper Margate (Black)
## 2 2
## Margate (White) Masked/Glass Goby
## 2 2
## Midnight Parrotfish Molly Miller
## 3 2
## Mottled Mojarra Mutton Snapper
## 2 2
## Nassau Grouper Neon Goby
## 3 2
## Nurse Shark Ocean Surgeonfish
## 2 3
## Ocean Triggerfish Orangesided Goby
## 2 2
## Orangespotted Filefish Pallid Goby
## 2 2
## Palometa Peacock Flounder
## 2 3
## Pearl Blenny Pearly Razorfish
## 2 2
## Peppermint Bass Peppermint Goby
## 2 2
## Permit Pluma
## 2 2
## Porcupinefish Porkfish
## 2 2
## Princess Parrotfish Puddingwife
## 3 2
## Purple Reeffish Queen Angelfish
## 2 3
## Queen Parrotfish Queen Triggerfish
## 3 2
## Rainbow Parrotfish Rainbow Runner
## 3 2
## Rainbow Wrasse Red Grouper
## 2 2
## Red Hind Redband Parrotfish
## 3 2
## Redlip Blenny Redspotted Hawkfish
## 2 2
## Redtail Parrotfish Reef Croaker
## 2 2
## Reef Squirrelfish Reel Butterflyfish
## 2 2
## Rock Beauty Rock Hind
## 3 3
## Rosy Blenny Rosy Razorfish
## 2 2
## Roughhead Blenny Round Scad
## 2 2
## Rusty Goby Saddled Blenny
## 2 2
## Sailfin Blenny Sailors Choice
## 2 2
## Sand Diver Sand Perch
## 2 2
## Sand Tilefish Sargassum Triggerfish
## 3 2
## Saucereye Porgy Scamp
## 2 2
## Schoolmaster Scrawled Cowfish
## 3 2
## Scrawled Filefish Seaweed Blenny
## 2 2
## Secretary Blenny Sergeant Major
## 2 3
## Sharknose Goby Sharksucker
## 2 2
## Sharpnose Puffer Sharptail Eel
## 2 2
## Sheepshead Sheepshead Porgy
## 2 2
## Shortstripe Goby Shy Hamlet
## 2 2
## Silver Porgy Silversides
## 2 3
## Slender Filefish Slippery Dick
## 2 2
## Smallmouth Grunt Smooth Trunkfish
## 2 3
## Southern Sennet Southern Stingray
## 2 2
## Spanish Grunt Spanish Hogfish
## 2 3
## Spanish Mackerel Spiny Blenny
## 2 2
## Sponge Cardinalfish Spotfin Butterflyfish
## 2 3
## Spotfin Hogfish Spotlight Goby
## 2 2
## Spottail Pinfish Spotted Drum
## 2 2
## Spotted Eagle Ray Spotted Goatfish
## 2 2
## Spotted Moray Spotted Scorpionfish
## 2 2
## Spotted Trunkfish Squirrelfish
## 2 3
## Stoplight Parrotfish Striped Grunt
## 3 2
## Striped Parrotfish Sunshinefish
## 3 2
## Tan Hamlet Tarpon
## 2 3
## Threeline Basslet Threespot Damselfish
## 2 3
## Tiger Grouper Tobaccofish
## 2 2
## Tomtate Trumpetfish
## 2 3
## Twospot Cardinalfish Unidentified juvenile Grunt
## 2 2
## Unidentified Sea Turtle Unidentified Triplefin
## 2 2
## White Grunt Whitespotted Filefish
## 2 2
## Whitestar Cardinalfish Wrasse Bleny
## 2 2
## Yellow Goatfish Yellow Jack
## 1 2
## Yellow Stingray Yellowbelly Hamlet
## 2 2
## Yellowcheek Wrasse Yellowfin Grouper
## 2 2
## Yellowfin Mojarra Yellowhead Jawfish
## 2 2
## Yellowhead Wrasse Yellowline Goby
## 2 3
## Yellowmouth Grouper Yellownose Goby
## 2 2
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 2 2
## Yellowtail Damselfish Yellowtail Hamlet
## 3 2
## Yellowtail Reeffish Yellowtail Snapper
## 2 3
##
## Within cluster sum of squares by cluster:
## [1] 5.646235 17.475955 26.844551 0.000000
## (between_SS / total_SS = 89.8 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"
## [1] 3 197 45 1## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.413 0.701 4.98 0.168## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_98
## 1 3.3708185 -5.838370 2.7750663 4 3
## 2 -0.4338479 0.121128 0.1087986 5 197
## 3 1.6524260 0.121128 1.5708361 5 45
## 4 0.9964154 -11.797868 1.1111112 3 1## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.00 5 2
## Arrow Blenny 0.00 5 2
## Atlantic Spadefish 0.40 5 2
## Balloonfish 0.60 5 2
## Banded Butterflyfish 1.25 5 3
## Bandtail Puffer 0.00 5 22000 K-Means
## K-means clustering with 4 clusters of sizes 1, 13, 21, 211
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 1.7907923 -15.62062947
## 2 3.2617558 0.06375767
## 3 1.6265220 0.06375767
## 4 -0.3713298 0.06375767
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 4 4
## Atlantic Spadefish Balloonfish
## 4 4
## Banded Butterflyfish Bandtail Puffer
## 3 4
## Bar Jack Barred Cardinalfish
## 4 4
## Barred Hamlet Beaugregory
## 4 4
## Belted Cardinalfish Belted Sandfish
## 4 4
## Bicolor Damselfish Black Durgon
## 3 4
## Black Grouper Black Hamlet
## 4 4
## Black Jack Blackbar Soldierfish
## 4 4
## Blackcap Basslet Blackear Wrasse
## 4 2
## Blackfin Snapper Blue Angelfish
## 4 4
## Blue Chromis Blue Goby
## 2 4
## Blue Hamlet Blue Parrotfish
## 4 4
## Blue Runner Blue Tang
## 4 4
## Bluehead Bluelip Parrotfish
## 4 4
## Bluespotted Cornetfish Bluestriped Grunt
## 4 4
## Boga Bonefish
## 4 4
## Bonnetmouth Bridled Goby
## 4 4
## Brown Chromis Brown Garden Eel
## 1 4
## Bucktooth Parrotfish Butter Hamlet
## 4 4
## Caesar Grunt Cero
## 4 4
## Chain Moray Chalk Bass
## 4 4
## Cherubfish Chub (Bermuda/Yellow)
## 4 4
## Cleaning Goby Clown Wrasse
## 4 4
## Cocoa Damselfish Colon Goby
## 4 4
## Common Snook Coney
## 3 4
## Cottonwick Creole Wrasse
## 2 4
## Creole-fish Crevalle Jack
## 4 4
## Cubbyu Cubera Snapper
## 4 4
## Darkheaded Blenny Diamond Blenny
## 4 4
## Doctorfish Dog Snapper
## 4 4
## Dusky Damselfish Dusky Squirrelfish
## 2 3
## Eyed Flounder Fairy Basslet
## 4 2
## Flamefish Flying Gurnard
## 4 4
## Foureye Butterflyfish French Angelfish
## 2 3
## French Grunt Gag
## 4 4
## Glasseye Snapper Glassy Sweeper
## 4 3
## Goldentail Moray Goldspot Goby
## 4 4
## Goliath Grouper (Jewfish) Gray Angelfish
## 4 4
## Gray Snapper Gray Triggerfish
## 4 4
## Graysby Great Barracuda
## 4 3
## Greater Amberjack Greater Soapfish
## 4 4
## Green Moray Green Razorfish
## 4 4
## Green Sea Turtle Greenblotch Parrotfish
## 4 4
## Hairy Blenny Harlequin Bass
## 4 4
## Hawksbill Sea Turtle Highhat
## 4 4
## Hogfish Honeycomb Cowfish
## 4 4
## Horse-eye Jack Houndfish
## 4 4
## Hovering Goby Hybrid Hamlet
## 4 4
## Indigo Hamlet Jackknife Fish
## 4 4
## Jolthead Porgy Lancer Dragonet
## 4 4
## Lane Snapper Lantern Bass
## 4 4
## Lionfish Loggerhead Sea Turtle
## 4 4
## Longfin Damselfish Longjaw Squirrelfish
## 4 4
## Longsnout Butterflyfish Longspine Squirrelfish
## 4 4
## Mahogany Snapper Margate (Black)
## 4 3
## Margate (White) Masked/Glass Goby
## 4 4
## Midnight Parrotfish Molly Miller
## 3 4
## Mottled Mojarra Mutton Snapper
## 4 3
## Nassau Grouper Neon Goby
## 4 4
## Nurse Shark Ocean Surgeonfish
## 4 3
## Ocean Triggerfish Orangesided Goby
## 4 4
## Orangespotted Filefish Pallid Goby
## 4 4
## Palometa Peacock Flounder
## 4 4
## Pearl Blenny Pearly Razorfish
## 4 4
## Peppermint Bass Peppermint Goby
## 4 4
## Permit Pluma
## 4 4
## Porcupinefish Porkfish
## 4 4
## Princess Parrotfish Puddingwife
## 4 4
## Purple Reeffish Queen Angelfish
## 4 4
## Queen Parrotfish Queen Triggerfish
## 3 4
## Rainbow Parrotfish Rainbow Runner
## 2 4
## Rainbow Wrasse Red Grouper
## 4 3
## Red Hind Redband Parrotfish
## 4 4
## Redlip Blenny Redspotted Hawkfish
## 4 4
## Redtail Parrotfish Reef Croaker
## 2 4
## Reef Squirrelfish Reel Butterflyfish
## 2 4
## Rock Beauty Rock Hind
## 3 4
## Rosy Blenny Rosy Razorfish
## 4 4
## Roughhead Blenny Round Scad
## 4 4
## Rusty Goby Saddled Blenny
## 4 4
## Sailfin Blenny Sailors Choice
## 4 4
## Sand Diver Sand Perch
## 4 4
## Sand Tilefish Sargassum Triggerfish
## 3 4
## Saucereye Porgy Scamp
## 4 4
## Schoolmaster Scrawled Cowfish
## 2 4
## Scrawled Filefish Seaweed Blenny
## 4 4
## Secretary Blenny Sergeant Major
## 4 2
## Sharknose Goby Sharksucker
## 4 4
## Sharpnose Puffer Sharptail Eel
## 4 4
## Sheepshead Sheepshead Porgy
## 4 4
## Shortstripe Goby Shy Hamlet
## 4 4
## Silver Porgy Silversides
## 4 4
## Slender Filefish Slippery Dick
## 4 4
## Smallmouth Grunt Smooth Trunkfish
## 4 3
## Southern Sennet Southern Stingray
## 4 4
## Spanish Grunt Spanish Hogfish
## 4 4
## Spanish Mackerel Spiny Blenny
## 3 4
## Sponge Cardinalfish Spotfin Butterflyfish
## 4 3
## Spotfin Hogfish Spotlight Goby
## 3 4
## Spottail Pinfish Spotted Drum
## 4 4
## Spotted Eagle Ray Spotted Goatfish
## 4 4
## Spotted Moray Spotted Scorpionfish
## 4 4
## Spotted Trunkfish Squirrelfish
## 4 2
## Stoplight Parrotfish Striped Grunt
## 4 4
## Striped Parrotfish Sunshinefish
## 4 4
## Tan Hamlet Tarpon
## 4 4
## Threeline Basslet Threespot Damselfish
## 4 2
## Tiger Grouper Tobaccofish
## 4 4
## Tomtate Trumpetfish
## 4 4
## Twospot Cardinalfish Unidentified juvenile Grunt
## 4 4
## Unidentified Sea Turtle Unidentified Triplefin
## 4 4
## White Grunt Whitespotted Filefish
## 4 4
## Whitestar Cardinalfish Wrasse Bleny
## 4 4
## Yellow Goatfish Yellow Jack
## 4 4
## Yellow Stingray Yellowbelly Hamlet
## 4 4
## Yellowcheek Wrasse Yellowfin Grouper
## 4 4
## Yellowfin Mojarra Yellowhead Jawfish
## 3 4
## Yellowhead Wrasse Yellowline Goby
## 4 4
## Yellowmouth Grouper Yellownose Goby
## 4 4
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 4 4
## Yellowtail Damselfish Yellowtail Hamlet
## 3 4
## Yellowtail Reeffish Yellowtail Snapper
## 4 4
##
## Within cluster sum of squares by cluster:
## [1] 0.000000 2.656586 5.140756 11.037111
## (between_SS / total_SS = 96.2 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"## [1] 1 13 21 211## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.338 0.705 7.99 0.191## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_00
## 1 1.7907923 -15.62062947 1.60000006 5 1
## 2 3.2617558 0.06375767 2.63654775 8 13
## 3 1.6265220 0.06375767 1.48424325 8 21
## 4 -0.3713298 0.06375767 0.07641189 8 211## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.000 8 4
## Arrow Blenny 0.375 8 4
## Atlantic Spadefish 0.000 8 4
## Balloonfish 0.375 8 4
## Banded Butterflyfish 1.725 8 3
## Bandtail Puffer 0.000 8 42002 K-Means
## K-means clustering with 4 clusters of sizes 28, 193, 1, 24
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 2.2038192 -2.3407942
## 2 -0.4705805 0.3360832
## 3 3.7637425 -7.7224331
## 4 1.0563062 0.3500253
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 2 2
## Atlantic Spadefish Balloonfish
## 2 2
## Banded Butterflyfish Bandtail Puffer
## 4 2
## Bar Jack Barred Cardinalfish
## 1 2
## Barred Hamlet Beaugregory
## 2 2
## Belted Cardinalfish Belted Sandfish
## 2 2
## Bicolor Damselfish Black Durgon
## 1 1
## Black Grouper Black Hamlet
## 4 2
## Black Jack Blackbar Soldierfish
## 2 2
## Blackcap Basslet Blackear Wrasse
## 2 2
## Blackfin Snapper Blue Angelfish
## 2 2
## Blue Chromis Blue Goby
## 4 2
## Blue Hamlet Blue Parrotfish
## 2 2
## Blue Runner Blue Tang
## 2 1
## Bluehead Bluelip Parrotfish
## 1 2
## Bluespotted Cornetfish Bluestriped Grunt
## 2 2
## Boga Bonefish
## 2 2
## Bonnetmouth Bridled Goby
## 2 2
## Brown Chromis Brown Garden Eel
## 3 4
## Bucktooth Parrotfish Butter Hamlet
## 2 2
## Caesar Grunt Cero
## 2 2
## Chain Moray Chalk Bass
## 2 2
## Cherubfish Chub (Bermuda/Yellow)
## 2 4
## Cleaning Goby Clown Wrasse
## 2 2
## Cocoa Damselfish Colon Goby
## 2 2
## Common Snook Coney
## 2 2
## Cottonwick Creole Wrasse
## 2 1
## Creole-fish Crevalle Jack
## 2 2
## Cubbyu Cubera Snapper
## 2 2
## Darkheaded Blenny Diamond Blenny
## 2 2
## Doctorfish Dog Snapper
## 2 2
## Dusky Damselfish Dusky Squirrelfish
## 1 2
## Eyed Flounder Fairy Basslet
## 2 1
## Flamefish Flying Gurnard
## 2 2
## Foureye Butterflyfish French Angelfish
## 1 4
## French Grunt Gag
## 1 2
## Glasseye Snapper Glassy Sweeper
## 2 2
## Goldentail Moray Goldspot Goby
## 2 2
## Goliath Grouper (Jewfish) Gray Angelfish
## 2 2
## Gray Snapper Gray Triggerfish
## 2 2
## Graysby Great Barracuda
## 2 4
## Greater Amberjack Greater Soapfish
## 2 4
## Green Moray Green Razorfish
## 2 2
## Green Sea Turtle Greenblotch Parrotfish
## 2 2
## Hairy Blenny Harlequin Bass
## 2 2
## Hawksbill Sea Turtle Highhat
## 2 2
## Hogfish Honeycomb Cowfish
## 2 2
## Horse-eye Jack Houndfish
## 2 2
## Hovering Goby Hybrid Hamlet
## 2 2
## Indigo Hamlet Jackknife Fish
## 1 2
## Jolthead Porgy Lancer Dragonet
## 2 2
## Lane Snapper Lantern Bass
## 4 2
## Lionfish Loggerhead Sea Turtle
## 2 2
## Longfin Damselfish Longjaw Squirrelfish
## 2 2
## Longsnout Butterflyfish Longspine Squirrelfish
## 2 1
## Mahogany Snapper Margate (Black)
## 2 2
## Margate (White) Masked/Glass Goby
## 2 2
## Midnight Parrotfish Molly Miller
## 4 2
## Mottled Mojarra Mutton Snapper
## 2 1
## Nassau Grouper Neon Goby
## 4 2
## Nurse Shark Ocean Surgeonfish
## 2 2
## Ocean Triggerfish Orangesided Goby
## 2 2
## Orangespotted Filefish Pallid Goby
## 2 2
## Palometa Peacock Flounder
## 2 1
## Pearl Blenny Pearly Razorfish
## 2 2
## Peppermint Bass Peppermint Goby
## 2 2
## Permit Pluma
## 2 2
## Porcupinefish Porkfish
## 2 2
## Princess Parrotfish Puddingwife
## 1 2
## Purple Reeffish Queen Angelfish
## 2 4
## Queen Parrotfish Queen Triggerfish
## 2 2
## Rainbow Parrotfish Rainbow Runner
## 4 2
## Rainbow Wrasse Red Grouper
## 4 2
## Red Hind Redband Parrotfish
## 1 2
## Redlip Blenny Redspotted Hawkfish
## 2 4
## Redtail Parrotfish Reef Croaker
## 2 2
## Reef Squirrelfish Reel Butterflyfish
## 2 2
## Rock Beauty Rock Hind
## 4 4
## Rosy Blenny Rosy Razorfish
## 2 2
## Roughhead Blenny Round Scad
## 2 2
## Rusty Goby Saddled Blenny
## 2 2
## Sailfin Blenny Sailors Choice
## 2 2
## Sand Diver Sand Perch
## 2 2
## Sand Tilefish Sargassum Triggerfish
## 4 2
## Saucereye Porgy Scamp
## 2 2
## Schoolmaster Scrawled Cowfish
## 1 2
## Scrawled Filefish Seaweed Blenny
## 2 2
## Secretary Blenny Sergeant Major
## 2 1
## Sharknose Goby Sharksucker
## 2 2
## Sharpnose Puffer Sharptail Eel
## 2 2
## Sheepshead Sheepshead Porgy
## 2 2
## Shortstripe Goby Shy Hamlet
## 2 2
## Silver Porgy Silversides
## 2 2
## Slender Filefish Slippery Dick
## 2 2
## Smallmouth Grunt Smooth Trunkfish
## 2 4
## Southern Sennet Southern Stingray
## 2 2
## Spanish Grunt Spanish Hogfish
## 2 1
## Spanish Mackerel Spiny Blenny
## 2 2
## Sponge Cardinalfish Spotfin Butterflyfish
## 2 1
## Spotfin Hogfish Spotlight Goby
## 2 2
## Spottail Pinfish Spotted Drum
## 2 4
## Spotted Eagle Ray Spotted Goatfish
## 2 2
## Spotted Moray Spotted Scorpionfish
## 2 2
## Spotted Trunkfish Squirrelfish
## 1 1
## Stoplight Parrotfish Striped Grunt
## 1 2
## Striped Parrotfish Sunshinefish
## 1 2
## Tan Hamlet Tarpon
## 2 1
## Threeline Basslet Threespot Damselfish
## 2 1
## Tiger Grouper Tobaccofish
## 2 2
## Tomtate Trumpetfish
## 2 1
## Twospot Cardinalfish Unidentified juvenile Grunt
## 2 2
## Unidentified Sea Turtle Unidentified Triplefin
## 2 2
## White Grunt Whitespotted Filefish
## 2 2
## Whitestar Cardinalfish Wrasse Bleny
## 2 2
## Yellow Goatfish Yellow Jack
## 4 2
## Yellow Stingray Yellowbelly Hamlet
## 2 2
## Yellowcheek Wrasse Yellowfin Grouper
## 2 2
## Yellowfin Mojarra Yellowhead Jawfish
## 2 2
## Yellowhead Wrasse Yellowline Goby
## 4 4
## Yellowmouth Grouper Yellownose Goby
## 2 2
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 2 2
## Yellowtail Damselfish Yellowtail Hamlet
## 4 2
## Yellowtail Reeffish Yellowtail Snapper
## 2 1
##
## Within cluster sum of squares by cluster:
## [1] 10.408610 15.595991 0.000000 6.523836
## (between_SS / total_SS = 93.4 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"## [1] 28 193 1 24## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.432 0.749 6.87 0.372## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_02
## 1 2.2038192 -2.3407942 2.08224209 6.000000 28
## 2 -0.4705805 0.3360832 0.08018755 6.994819 193
## 3 3.7637425 -7.7224331 3.25000003 4.000000 1
## 4 1.0563062 0.3500253 1.22321432 7.000000 24## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.0000000 7 2
## Arrow Blenny 0.0000000 7 2
## Atlantic Spadefish 0.0000000 7 2
## Balloonfish 0.1428571 7 2
## Banded Butterflyfish 1.4285714 7 4
## Bandtail Puffer 0.1428571 7 22004 K-Means
## K-means clustering with 4 clusters of sizes 201, 25, 1, 19
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 -0.4138564 0.06375767
## 2 1.0483430 0.06375767
## 3 1.0454268 -15.62062947
## 4 2.9437439 0.06375767
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 1 1
## Atlantic Spadefish Balloonfish
## 1 1
## Banded Butterflyfish Bandtail Puffer
## 1 1
## Bar Jack Barred Cardinalfish
## 1 4
## Barred Hamlet Beaugregory
## 1 1
## Belted Cardinalfish Belted Sandfish
## 1 1
## Bicolor Damselfish Black Durgon
## 1 1
## Black Grouper Black Hamlet
## 1 1
## Black Jack Blackbar Soldierfish
## 1 1
## Blackcap Basslet Blackear Wrasse
## 1 1
## Blackfin Snapper Blue Angelfish
## 1 2
## Blue Chromis Blue Goby
## 1 1
## Blue Hamlet Blue Parrotfish
## 1 1
## Blue Runner Blue Tang
## 2 2
## Bluehead Bluelip Parrotfish
## 1 1
## Bluespotted Cornetfish Bluestriped Grunt
## 1 1
## Boga Bonefish
## 1 1
## Bonnetmouth Bridled Goby
## 1 1
## Brown Chromis Brown Garden Eel
## 1 1
## Bucktooth Parrotfish Butter Hamlet
## 1 1
## Caesar Grunt Cero
## 1 2
## Chain Moray Chalk Bass
## 1 1
## Cherubfish Chub (Bermuda/Yellow)
## 1 1
## Cleaning Goby Clown Wrasse
## 1 1
## Cocoa Damselfish Colon Goby
## 1 1
## Common Snook Coney
## 1 1
## Cottonwick Creole Wrasse
## 1 2
## Creole-fish Crevalle Jack
## 1 1
## Cubbyu Cubera Snapper
## 4 1
## Darkheaded Blenny Diamond Blenny
## 1 1
## Doctorfish Dog Snapper
## 4 2
## Dusky Damselfish Dusky Squirrelfish
## 1 1
## Eyed Flounder Fairy Basslet
## 1 4
## Flamefish Flying Gurnard
## 1 1
## Foureye Butterflyfish French Angelfish
## 1 2
## French Grunt Gag
## 1 2
## Glasseye Snapper Glassy Sweeper
## 1 1
## Goldentail Moray Goldspot Goby
## 2 1
## Goliath Grouper (Jewfish) Gray Angelfish
## 1 1
## Gray Snapper Gray Triggerfish
## 1 1
## Graysby Great Barracuda
## 1 2
## Greater Amberjack Greater Soapfish
## 1 1
## Green Moray Green Razorfish
## 2 1
## Green Sea Turtle Greenblotch Parrotfish
## 1 1
## Hairy Blenny Harlequin Bass
## 1 1
## Hawksbill Sea Turtle Highhat
## 1 4
## Hogfish Honeycomb Cowfish
## 1 1
## Horse-eye Jack Houndfish
## 1 1
## Hovering Goby Hybrid Hamlet
## 1 1
## Indigo Hamlet Jackknife Fish
## 1 4
## Jolthead Porgy Lancer Dragonet
## 4 1
## Lane Snapper Lantern Bass
## 1 1
## Lionfish Loggerhead Sea Turtle
## 1 1
## Longfin Damselfish Longjaw Squirrelfish
## 4 4
## Longsnout Butterflyfish Longspine Squirrelfish
## 2 1
## Mahogany Snapper Margate (Black)
## 4 1
## Margate (White) Masked/Glass Goby
## 4 1
## Midnight Parrotfish Molly Miller
## 1 1
## Mottled Mojarra Mutton Snapper
## 1 2
## Nassau Grouper Neon Goby
## 1 1
## Nurse Shark Ocean Surgeonfish
## 1 1
## Ocean Triggerfish Orangesided Goby
## 1 1
## Orangespotted Filefish Pallid Goby
## 1 1
## Palometa Peacock Flounder
## 1 2
## Pearl Blenny Pearly Razorfish
## 1 1
## Peppermint Bass Peppermint Goby
## 1 1
## Permit Pluma
## 1 1
## Porcupinefish Porkfish
## 1 1
## Princess Parrotfish Puddingwife
## 1 1
## Purple Reeffish Queen Angelfish
## 1 2
## Queen Parrotfish Queen Triggerfish
## 1 4
## Rainbow Parrotfish Rainbow Runner
## 2 1
## Rainbow Wrasse Red Grouper
## 1 1
## Red Hind Redband Parrotfish
## 2 4
## Redlip Blenny Redspotted Hawkfish
## 1 1
## Redtail Parrotfish Reef Croaker
## 2 1
## Reef Squirrelfish Reel Butterflyfish
## 4 1
## Rock Beauty Rock Hind
## 4 1
## Rosy Blenny Rosy Razorfish
## 1 1
## Roughhead Blenny Round Scad
## 1 1
## Rusty Goby Saddled Blenny
## 1 1
## Sailfin Blenny Sailors Choice
## 1 1
## Sand Diver Sand Perch
## 1 1
## Sand Tilefish Sargassum Triggerfish
## 2 1
## Saucereye Porgy Scamp
## 1 2
## Schoolmaster Scrawled Cowfish
## 1 1
## Scrawled Filefish Seaweed Blenny
## 1 1
## Secretary Blenny Sergeant Major
## 1 1
## Sharknose Goby Sharksucker
## 1 1
## Sharpnose Puffer Sharptail Eel
## 1 1
## Sheepshead Sheepshead Porgy
## 1 1
## Shortstripe Goby Shy Hamlet
## 4 4
## Silver Porgy Silversides
## 1 1
## Slender Filefish Slippery Dick
## 1 1
## Smallmouth Grunt Smooth Trunkfish
## 1 1
## Southern Sennet Southern Stingray
## 1 1
## Spanish Grunt Spanish Hogfish
## 1 1
## Spanish Mackerel Spiny Blenny
## 1 1
## Sponge Cardinalfish Spotfin Butterflyfish
## 1 2
## Spotfin Hogfish Spotlight Goby
## 2 1
## Spottail Pinfish Spotted Drum
## 1 1
## Spotted Eagle Ray Spotted Goatfish
## 1 1
## Spotted Moray Spotted Scorpionfish
## 1 1
## Spotted Trunkfish Squirrelfish
## 1 1
## Stoplight Parrotfish Striped Grunt
## 1 1
## Striped Parrotfish Sunshinefish
## 1 4
## Tan Hamlet Tarpon
## 1 1
## Threeline Basslet Threespot Damselfish
## 1 4
## Tiger Grouper Tobaccofish
## 2 1
## Tomtate Trumpetfish
## 1 2
## Twospot Cardinalfish Unidentified juvenile Grunt
## 1 1
## Unidentified Sea Turtle Unidentified Triplefin
## 1 1
## White Grunt Whitespotted Filefish
## 1 1
## Whitestar Cardinalfish Wrasse Bleny
## 1 1
## Yellow Goatfish Yellow Jack
## 1 1
## Yellow Stingray Yellowbelly Hamlet
## 1 1
## Yellowcheek Wrasse Yellowfin Grouper
## 1 1
## Yellowfin Mojarra Yellowhead Jawfish
## 1 1
## Yellowhead Wrasse Yellowline Goby
## 1 1
## Yellowmouth Grouper Yellownose Goby
## 1 1
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 1 2
## Yellowtail Damselfish Yellowtail Hamlet
## 1 1
## Yellowtail Reeffish Yellowtail Snapper
## 3 1
##
## Within cluster sum of squares by cluster:
## [1] 5.242138 6.522784 0.000000 5.592959
## (between_SS / total_SS = 96.5 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"## [1] 201 25 1 19## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.312 0.658 7.00 0.0638## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_04
## 1 -0.4138564 0.06375767 0.04003791 7 201
## 2 1.0483430 0.06375767 1.00191841 7 25
## 3 1.0454268 -15.62062947 1.00000004 6 1
## 4 2.9437439 0.06375767 2.24877245 7 19## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.0000000 7 1
## Arrow Blenny 0.0000000 7 1
## Atlantic Spadefish 0.0000000 7 1
## Balloonfish 0.0000000 7 1
## Banded Butterflyfish 0.2857143 7 1
## Bandtail Puffer 0.0000000 7 12006 K-Means
## K-means clustering with 4 clusters of sizes 1, 201, 25, 19
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 1.4543713 -15.62062947
## 2 -0.4215216 0.06375767
## 3 1.1259748 0.06375767
## 4 2.9011636 0.06375767
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 2 2
## Atlantic Spadefish Balloonfish
## 2 2
## Banded Butterflyfish Bandtail Puffer
## 2 2
## Bar Jack Barred Cardinalfish
## 2 4
## Barred Hamlet Beaugregory
## 2 2
## Belted Cardinalfish Belted Sandfish
## 3 2
## Bicolor Damselfish Black Durgon
## 2 2
## Black Grouper Black Hamlet
## 2 2
## Black Jack Blackbar Soldierfish
## 2 2
## Blackcap Basslet Blackear Wrasse
## 2 3
## Blackfin Snapper Blue Angelfish
## 2 2
## Blue Chromis Blue Goby
## 2 2
## Blue Hamlet Blue Parrotfish
## 2 2
## Blue Runner Blue Tang
## 3 2
## Bluehead Bluelip Parrotfish
## 2 2
## Bluespotted Cornetfish Bluestriped Grunt
## 2 2
## Boga Bonefish
## 2 2
## Bonnetmouth Bridled Goby
## 2 2
## Brown Chromis Brown Garden Eel
## 2 2
## Bucktooth Parrotfish Butter Hamlet
## 2 2
## Caesar Grunt Cero
## 2 2
## Chain Moray Chalk Bass
## 2 2
## Cherubfish Chub (Bermuda/Yellow)
## 2 2
## Cleaning Goby Clown Wrasse
## 2 2
## Cocoa Damselfish Colon Goby
## 2 2
## Common Snook Coney
## 2 2
## Cottonwick Creole Wrasse
## 2 2
## Creole-fish Crevalle Jack
## 2 2
## Cubbyu Cubera Snapper
## 4 2
## Darkheaded Blenny Diamond Blenny
## 2 2
## Doctorfish Dog Snapper
## 4 2
## Dusky Damselfish Dusky Squirrelfish
## 2 4
## Eyed Flounder Fairy Basslet
## 3 4
## Flamefish Flying Gurnard
## 2 2
## Foureye Butterflyfish French Angelfish
## 2 4
## French Grunt Gag
## 2 2
## Glasseye Snapper Glassy Sweeper
## 2 2
## Goldentail Moray Goldspot Goby
## 3 2
## Goliath Grouper (Jewfish) Gray Angelfish
## 2 2
## Gray Snapper Gray Triggerfish
## 2 2
## Graysby Great Barracuda
## 2 3
## Greater Amberjack Greater Soapfish
## 2 2
## Green Moray Green Razorfish
## 3 3
## Green Sea Turtle Greenblotch Parrotfish
## 2 2
## Hairy Blenny Harlequin Bass
## 2 2
## Hawksbill Sea Turtle Highhat
## 2 2
## Hogfish Honeycomb Cowfish
## 2 2
## Horse-eye Jack Houndfish
## 2 2
## Hovering Goby Hybrid Hamlet
## 2 2
## Indigo Hamlet Jackknife Fish
## 2 3
## Jolthead Porgy Lancer Dragonet
## 4 2
## Lane Snapper Lantern Bass
## 2 2
## Lionfish Loggerhead Sea Turtle
## 2 2
## Longfin Damselfish Longjaw Squirrelfish
## 4 4
## Longsnout Butterflyfish Longspine Squirrelfish
## 3 3
## Mahogany Snapper Margate (Black)
## 4 2
## Margate (White) Masked/Glass Goby
## 4 2
## Midnight Parrotfish Molly Miller
## 2 2
## Mottled Mojarra Mutton Snapper
## 2 4
## Nassau Grouper Neon Goby
## 2 2
## Nurse Shark Ocean Surgeonfish
## 2 2
## Ocean Triggerfish Orangesided Goby
## 2 2
## Orangespotted Filefish Pallid Goby
## 2 2
## Palometa Peacock Flounder
## 2 3
## Pearl Blenny Pearly Razorfish
## 2 2
## Peppermint Bass Peppermint Goby
## 2 2
## Permit Pluma
## 2 2
## Porcupinefish Porkfish
## 2 3
## Princess Parrotfish Puddingwife
## 2 3
## Purple Reeffish Queen Angelfish
## 2 3
## Queen Parrotfish Queen Triggerfish
## 2 4
## Rainbow Parrotfish Rainbow Runner
## 3 2
## Rainbow Wrasse Red Grouper
## 2 3
## Red Hind Redband Parrotfish
## 2 4
## Redlip Blenny Redspotted Hawkfish
## 2 2
## Redtail Parrotfish Reef Croaker
## 2 2
## Reef Squirrelfish Reel Butterflyfish
## 4 3
## Rock Beauty Rock Hind
## 4 2
## Rosy Blenny Rosy Razorfish
## 2 2
## Roughhead Blenny Round Scad
## 2 2
## Rusty Goby Saddled Blenny
## 2 2
## Sailfin Blenny Sailors Choice
## 2 2
## Sand Diver Sand Perch
## 2 2
## Sand Tilefish Sargassum Triggerfish
## 3 2
## Saucereye Porgy Scamp
## 2 3
## Schoolmaster Scrawled Cowfish
## 3 2
## Scrawled Filefish Seaweed Blenny
## 2 2
## Secretary Blenny Sergeant Major
## 2 2
## Sharknose Goby Sharksucker
## 2 2
## Sharpnose Puffer Sharptail Eel
## 2 2
## Sheepshead Sheepshead Porgy
## 2 2
## Shortstripe Goby Shy Hamlet
## 4 2
## Silver Porgy Silversides
## 2 2
## Slender Filefish Slippery Dick
## 2 2
## Smallmouth Grunt Smooth Trunkfish
## 2 2
## Southern Sennet Southern Stingray
## 2 2
## Spanish Grunt Spanish Hogfish
## 2 2
## Spanish Mackerel Spiny Blenny
## 2 2
## Sponge Cardinalfish Spotfin Butterflyfish
## 2 4
## Spotfin Hogfish Spotlight Goby
## 3 2
## Spottail Pinfish Spotted Drum
## 2 2
## Spotted Eagle Ray Spotted Goatfish
## 2 2
## Spotted Moray Spotted Scorpionfish
## 2 2
## Spotted Trunkfish Squirrelfish
## 2 2
## Stoplight Parrotfish Striped Grunt
## 2 2
## Striped Parrotfish Sunshinefish
## 2 4
## Tan Hamlet Tarpon
## 2 2
## Threeline Basslet Threespot Damselfish
## 2 3
## Tiger Grouper Tobaccofish
## 2 2
## Tomtate Trumpetfish
## 2 2
## Twospot Cardinalfish Unidentified juvenile Grunt
## 2 2
## Unidentified Sea Turtle Unidentified Triplefin
## 2 2
## White Grunt Whitespotted Filefish
## 2 2
## Whitestar Cardinalfish Wrasse Bleny
## 2 2
## Yellow Goatfish Yellow Jack
## 2 2
## Yellow Stingray Yellowbelly Hamlet
## 2 2
## Yellowcheek Wrasse Yellowfin Grouper
## 2 2
## Yellowfin Mojarra Yellowhead Jawfish
## 2 3
## Yellowhead Wrasse Yellowline Goby
## 2 2
## Yellowmouth Grouper Yellownose Goby
## 2 2
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 2 3
## Yellowtail Damselfish Yellowtail Hamlet
## 2 2
## Yellowtail Reeffish Yellowtail Snapper
## 1 2
##
## Within cluster sum of squares by cluster:
## [1] 0.000000 5.995451 5.379587 4.182251
## (between_SS / total_SS = 96.8 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"## [1] 1 201 25 19## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.324 0.661 8.00 0.0638## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_06
## 1 1.4543713 -15.62062947 1.28571423 7 1
## 2 -0.4215216 0.06375767 0.04560531 8 201
## 3 1.1259748 0.06375767 1.06861900 8 25
## 4 2.9011636 0.06375767 2.24215477 8 19## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.000 8 2
## Arrow Blenny 0.000 8 2
## Atlantic Spadefish 0.125 8 2
## Balloonfish 0.000 8 2
## Banded Butterflyfish 0.125 8 2
## Bandtail Puffer 0.000 8 22008 K-Means
## K-means clustering with 4 clusters of sizes 1, 27, 195, 23
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 2.3529504 -15.62062947
## 2 0.9355029 0.06375767
## 3 -0.4532149 0.06375767
## 4 2.6419727 0.06375767
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 3 3
## Atlantic Spadefish Balloonfish
## 3 3
## Banded Butterflyfish Bandtail Puffer
## 2 3
## Bar Jack Barred Cardinalfish
## 3 4
## Barred Hamlet Beaugregory
## 3 3
## Belted Cardinalfish Belted Sandfish
## 3 3
## Bicolor Damselfish Black Durgon
## 3 2
## Black Grouper Black Hamlet
## 3 3
## Black Jack Blackbar Soldierfish
## 3 3
## Blackcap Basslet Blackear Wrasse
## 3 3
## Blackfin Snapper Blue Angelfish
## 3 3
## Blue Chromis Blue Goby
## 3 3
## Blue Hamlet Blue Parrotfish
## 3 3
## Blue Runner Blue Tang
## 3 3
## Bluehead Bluelip Parrotfish
## 3 3
## Bluespotted Cornetfish Bluestriped Grunt
## 3 3
## Boga Bonefish
## 3 3
## Bonnetmouth Bridled Goby
## 3 3
## Brown Chromis Brown Garden Eel
## 3 3
## Bucktooth Parrotfish Butter Hamlet
## 3 3
## Caesar Grunt Cero
## 3 3
## Chain Moray Chalk Bass
## 3 3
## Cherubfish Chub (Bermuda/Yellow)
## 3 3
## Cleaning Goby Clown Wrasse
## 3 3
## Cocoa Damselfish Colon Goby
## 3 3
## Common Snook Coney
## 3 3
## Cottonwick Creole Wrasse
## 3 4
## Creole-fish Crevalle Jack
## 3 3
## Cubbyu Cubera Snapper
## 4 3
## Darkheaded Blenny Diamond Blenny
## 3 3
## Doctorfish Dog Snapper
## 4 3
## Dusky Damselfish Dusky Squirrelfish
## 2 3
## Eyed Flounder Fairy Basslet
## 2 4
## Flamefish Flying Gurnard
## 3 3
## Foureye Butterflyfish French Angelfish
## 3 4
## French Grunt Gag
## 3 2
## Glasseye Snapper Glassy Sweeper
## 3 3
## Goldentail Moray Goldspot Goby
## 3 3
## Goliath Grouper (Jewfish) Gray Angelfish
## 3 3
## Gray Snapper Gray Triggerfish
## 3 3
## Graysby Great Barracuda
## 3 4
## Greater Amberjack Greater Soapfish
## 3 3
## Green Moray Green Razorfish
## 2 2
## Green Sea Turtle Greenblotch Parrotfish
## 2 3
## Hairy Blenny Harlequin Bass
## 3 3
## Hawksbill Sea Turtle Highhat
## 2 4
## Hogfish Honeycomb Cowfish
## 3 3
## Horse-eye Jack Houndfish
## 3 3
## Hovering Goby Hybrid Hamlet
## 3 3
## Indigo Hamlet Jackknife Fish
## 3 2
## Jolthead Porgy Lancer Dragonet
## 4 3
## Lane Snapper Lantern Bass
## 3 3
## Lionfish Loggerhead Sea Turtle
## 3 3
## Longfin Damselfish Longjaw Squirrelfish
## 4 4
## Longsnout Butterflyfish Longspine Squirrelfish
## 2 3
## Mahogany Snapper Margate (Black)
## 4 3
## Margate (White) Masked/Glass Goby
## 4 3
## Midnight Parrotfish Molly Miller
## 3 3
## Mottled Mojarra Mutton Snapper
## 3 1
## Nassau Grouper Neon Goby
## 3 3
## Nurse Shark Ocean Surgeonfish
## 3 3
## Ocean Triggerfish Orangesided Goby
## 3 3
## Orangespotted Filefish Pallid Goby
## 3 3
## Palometa Peacock Flounder
## 3 4
## Pearl Blenny Pearly Razorfish
## 3 3
## Peppermint Bass Peppermint Goby
## 3 3
## Permit Pluma
## 3 3
## Porcupinefish Porkfish
## 3 3
## Princess Parrotfish Puddingwife
## 3 2
## Purple Reeffish Queen Angelfish
## 3 2
## Queen Parrotfish Queen Triggerfish
## 3 4
## Rainbow Parrotfish Rainbow Runner
## 2 3
## Rainbow Wrasse Red Grouper
## 3 2
## Red Hind Redband Parrotfish
## 2 4
## Redlip Blenny Redspotted Hawkfish
## 3 3
## Redtail Parrotfish Reef Croaker
## 2 3
## Reef Squirrelfish Reel Butterflyfish
## 4 2
## Rock Beauty Rock Hind
## 4 3
## Rosy Blenny Rosy Razorfish
## 3 2
## Roughhead Blenny Round Scad
## 3 3
## Rusty Goby Saddled Blenny
## 3 3
## Sailfin Blenny Sailors Choice
## 3 2
## Sand Diver Sand Perch
## 3 3
## Sand Tilefish Sargassum Triggerfish
## 2 3
## Saucereye Porgy Scamp
## 3 4
## Schoolmaster Scrawled Cowfish
## 3 3
## Scrawled Filefish Seaweed Blenny
## 3 3
## Secretary Blenny Sergeant Major
## 3 3
## Sharknose Goby Sharksucker
## 3 3
## Sharpnose Puffer Sharptail Eel
## 3 3
## Sheepshead Sheepshead Porgy
## 3 3
## Shortstripe Goby Shy Hamlet
## 4 2
## Silver Porgy Silversides
## 3 3
## Slender Filefish Slippery Dick
## 3 3
## Smallmouth Grunt Smooth Trunkfish
## 3 3
## Southern Sennet Southern Stingray
## 3 3
## Spanish Grunt Spanish Hogfish
## 3 2
## Spanish Mackerel Spiny Blenny
## 3 3
## Sponge Cardinalfish Spotfin Butterflyfish
## 3 4
## Spotfin Hogfish Spotlight Goby
## 2 3
## Spottail Pinfish Spotted Drum
## 3 3
## Spotted Eagle Ray Spotted Goatfish
## 3 3
## Spotted Moray Spotted Scorpionfish
## 3 3
## Spotted Trunkfish Squirrelfish
## 3 3
## Stoplight Parrotfish Striped Grunt
## 3 3
## Striped Parrotfish Sunshinefish
## 3 4
## Tan Hamlet Tarpon
## 3 2
## Threeline Basslet Threespot Damselfish
## 3 4
## Tiger Grouper Tobaccofish
## 3 3
## Tomtate Trumpetfish
## 3 3
## Twospot Cardinalfish Unidentified juvenile Grunt
## 3 3
## Unidentified Sea Turtle Unidentified Triplefin
## 2 3
## White Grunt Whitespotted Filefish
## 3 3
## Whitestar Cardinalfish Wrasse Bleny
## 3 3
## Yellow Goatfish Yellow Jack
## 3 3
## Yellow Stingray Yellowbelly Hamlet
## 3 3
## Yellowcheek Wrasse Yellowfin Grouper
## 3 3
## Yellowfin Mojarra Yellowhead Jawfish
## 2 3
## Yellowhead Wrasse Yellowline Goby
## 3 3
## Yellowmouth Grouper Yellownose Goby
## 3 3
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 3 3
## Yellowtail Damselfish Yellowtail Hamlet
## 3 3
## Yellowtail Reeffish Yellowtail Snapper
## 3 3
##
## Within cluster sum of squares by cluster:
## [1] 0.000000 3.924964 5.122044 6.192959
## (between_SS / total_SS = 96.9 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"## [1] 1 27 195 23## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.373 0.725 8.00 0.0638## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_08
## 1 2.3529504 -15.62062947 2.08027203 7 1
## 2 0.9355029 0.06375767 1.05204472 8 27
## 3 -0.4532149 0.06375767 0.04465814 8 195
## 4 2.6419727 0.06375767 2.28993105 8 23## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.000000 8 3
## Arrow Blenny 0.000000 8 3
## Atlantic Spadefish 0.000000 8 3
## Balloonfish 0.000000 8 3
## Banded Butterflyfish 1.627083 8 2
## Bandtail Puffer 0.000000 8 32010 K-Means
## K-means clustering with 4 clusters of sizes 164, 28, 6, 48
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 -0.5896422 0.1501359
## 2 2.1572434 0.1501359
## 3 1.5100680 -6.0054364
## 4 0.5674605 0.1501359
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 1 1
## Atlantic Spadefish Balloonfish
## 1 1
## Banded Butterflyfish Bandtail Puffer
## 1 4
## Bar Jack Barred Cardinalfish
## 1 2
## Barred Hamlet Beaugregory
## 1 1
## Belted Cardinalfish Belted Sandfish
## 1 1
## Bicolor Damselfish Black Durgon
## 1 1
## Black Grouper Black Hamlet
## 1 1
## Black Jack Blackbar Soldierfish
## 1 1
## Blackcap Basslet Blackear Wrasse
## 4 3
## Blackfin Snapper Blue Angelfish
## 1 1
## Blue Chromis Blue Goby
## 1 4
## Blue Hamlet Blue Parrotfish
## 1 1
## Blue Runner Blue Tang
## 2 2
## Bluehead Bluelip Parrotfish
## 1 1
## Bluespotted Cornetfish Bluestriped Grunt
## 1 1
## Boga Bonefish
## 1 1
## Bonnetmouth Bridled Goby
## 1 4
## Brown Chromis Brown Garden Eel
## 1 1
## Bucktooth Parrotfish Butter Hamlet
## 1 4
## Caesar Grunt Cero
## 1 1
## Chain Moray Chalk Bass
## 1 1
## Cherubfish Chub (Bermuda/Yellow)
## 1 1
## Cleaning Goby Clown Wrasse
## 1 1
## Cocoa Damselfish Colon Goby
## 1 1
## Common Snook Coney
## 4 4
## Cottonwick Creole Wrasse
## 4 2
## Creole-fish Crevalle Jack
## 1 1
## Cubbyu Cubera Snapper
## 2 1
## Darkheaded Blenny Diamond Blenny
## 1 1
## Doctorfish Dog Snapper
## 2 4
## Dusky Damselfish Dusky Squirrelfish
## 4 4
## Eyed Flounder Fairy Basslet
## 4 2
## Flamefish Flying Gurnard
## 1 1
## Foureye Butterflyfish French Angelfish
## 1 4
## French Grunt Gag
## 2 4
## Glasseye Snapper Glassy Sweeper
## 1 3
## Goldentail Moray Goldspot Goby
## 1 1
## Goliath Grouper (Jewfish) Gray Angelfish
## 1 4
## Gray Snapper Gray Triggerfish
## 4 1
## Graysby Great Barracuda
## 4 4
## Greater Amberjack Greater Soapfish
## 1 4
## Green Moray Green Razorfish
## 3 4
## Green Sea Turtle Greenblotch Parrotfish
## 1 1
## Hairy Blenny Harlequin Bass
## 1 1
## Hawksbill Sea Turtle Highhat
## 1 4
## Hogfish Honeycomb Cowfish
## 1 1
## Horse-eye Jack Houndfish
## 1 1
## Hovering Goby Hybrid Hamlet
## 1 1
## Indigo Hamlet Jackknife Fish
## 1 2
## Jolthead Porgy Lancer Dragonet
## 2 2
## Lane Snapper Lantern Bass
## 4 4
## Lionfish Loggerhead Sea Turtle
## 4 1
## Longfin Damselfish Longjaw Squirrelfish
## 2 2
## Longsnout Butterflyfish Longspine Squirrelfish
## 4 4
## Mahogany Snapper Margate (Black)
## 2 1
## Margate (White) Masked/Glass Goby
## 2 1
## Midnight Parrotfish Molly Miller
## 4 2
## Mottled Mojarra Mutton Snapper
## 1 4
## Nassau Grouper Neon Goby
## 1 1
## Nurse Shark Ocean Surgeonfish
## 1 1
## Ocean Triggerfish Orangesided Goby
## 1 1
## Orangespotted Filefish Pallid Goby
## 4 1
## Palometa Peacock Flounder
## 1 2
## Pearl Blenny Pearly Razorfish
## 1 1
## Peppermint Bass Peppermint Goby
## 1 1
## Permit Pluma
## 1 1
## Porcupinefish Porkfish
## 1 1
## Princess Parrotfish Puddingwife
## 1 4
## Purple Reeffish Queen Angelfish
## 1 4
## Queen Parrotfish Queen Triggerfish
## 1 2
## Rainbow Parrotfish Rainbow Runner
## 4 1
## Rainbow Wrasse Red Grouper
## 1 2
## Red Hind Redband Parrotfish
## 4 2
## Redlip Blenny Redspotted Hawkfish
## 1 1
## Redtail Parrotfish Reef Croaker
## 3 1
## Reef Squirrelfish Reel Butterflyfish
## 2 4
## Rock Beauty Rock Hind
## 2 1
## Rosy Blenny Rosy Razorfish
## 1 1
## Roughhead Blenny Round Scad
## 1 1
## Rusty Goby Saddled Blenny
## 1 1
## Sailfin Blenny Sailors Choice
## 1 1
## Sand Diver Sand Perch
## 1 1
## Sand Tilefish Sargassum Triggerfish
## 4 1
## Saucereye Porgy Scamp
## 1 4
## Schoolmaster Scrawled Cowfish
## 1 1
## Scrawled Filefish Seaweed Blenny
## 1 1
## Secretary Blenny Sergeant Major
## 1 2
## Sharknose Goby Sharksucker
## 1 1
## Sharpnose Puffer Sharptail Eel
## 1 1
## Sheepshead Sheepshead Porgy
## 1 1
## Shortstripe Goby Shy Hamlet
## 3 4
## Silver Porgy Silversides
## 1 1
## Slender Filefish Slippery Dick
## 2 1
## Smallmouth Grunt Smooth Trunkfish
## 1 4
## Southern Sennet Southern Stingray
## 1 1
## Spanish Grunt Spanish Hogfish
## 1 4
## Spanish Mackerel Spiny Blenny
## 1 1
## Sponge Cardinalfish Spotfin Butterflyfish
## 1 2
## Spotfin Hogfish Spotlight Goby
## 2 4
## Spottail Pinfish Spotted Drum
## 1 1
## Spotted Eagle Ray Spotted Goatfish
## 1 1
## Spotted Moray Spotted Scorpionfish
## 1 1
## Spotted Trunkfish Squirrelfish
## 1 4
## Stoplight Parrotfish Striped Grunt
## 1 1
## Striped Parrotfish Sunshinefish
## 1 2
## Tan Hamlet Tarpon
## 1 1
## Threeline Basslet Threespot Damselfish
## 1 2
## Tiger Grouper Tobaccofish
## 1 1
## Tomtate Trumpetfish
## 1 4
## Twospot Cardinalfish Unidentified juvenile Grunt
## 1 1
## Unidentified Sea Turtle Unidentified Triplefin
## 1 1
## White Grunt Whitespotted Filefish
## 1 4
## Whitestar Cardinalfish Wrasse Bleny
## 1 1
## Yellow Goatfish Yellow Jack
## 4 1
## Yellow Stingray Yellowbelly Hamlet
## 4 1
## Yellowcheek Wrasse Yellowfin Grouper
## 1 1
## Yellowfin Mojarra Yellowhead Jawfish
## 1 4
## Yellowhead Wrasse Yellowline Goby
## 1 1
## Yellowmouth Grouper Yellownose Goby
## 1 1
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 1 4
## Yellowtail Damselfish Yellowtail Hamlet
## 4 1
## Yellowtail Reeffish Yellowtail Snapper
## 3 1
##
## Within cluster sum of squares by cluster:
## [1] 6.203541 7.437182 31.940858 6.155891
## (between_SS / total_SS = 89.4 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"## [1] 164 28 6 48## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.522 0.739 8.97 0.190## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_10
## 1 -0.5896422 0.1501359 0.08683377 9.000000 164
## 2 2.1572434 0.1501359 2.11596754 9.000000 28
## 3 1.5100680 -6.0054364 1.63789685 7.833333 6
## 4 0.5674605 0.1501359 0.94158951 9.000000 48## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.0000000 9 1
## Arrow Blenny 0.5000000 9 1
## Atlantic Spadefish 0.0000000 9 1
## Balloonfish 0.0000000 9 1
## Banded Butterflyfish 0.2222222 9 1
## Bandtail Puffer 0.5555556 9 42012 K-Means
## K-means clustering with 4 clusters of sizes 2, 40, 42, 162
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 0.8621329 -11.02288823
## 2 0.4481398 0.09035154
## 3 1.8956548 0.09035154
## 4 -0.6127615 0.09035154
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 4 4
## Atlantic Spadefish Balloonfish
## 4 4
## Banded Butterflyfish Bandtail Puffer
## 2 4
## Bar Jack Barred Cardinalfish
## 2 3
## Barred Hamlet Beaugregory
## 2 4
## Belted Cardinalfish Belted Sandfish
## 4 4
## Bicolor Damselfish Black Durgon
## 4 2
## Black Grouper Black Hamlet
## 4 4
## Black Jack Blackbar Soldierfish
## 4 3
## Blackcap Basslet Blackear Wrasse
## 3 2
## Blackfin Snapper Blue Angelfish
## 4 4
## Blue Chromis Blue Goby
## 4 4
## Blue Hamlet Blue Parrotfish
## 4 4
## Blue Runner Blue Tang
## 3 3
## Bluehead Bluelip Parrotfish
## 4 4
## Bluespotted Cornetfish Bluestriped Grunt
## 4 4
## Boga Bonefish
## 4 4
## Bonnetmouth Bridled Goby
## 4 4
## Brown Chromis Brown Garden Eel
## 4 4
## Bucktooth Parrotfish Butter Hamlet
## 4 2
## Caesar Grunt Cero
## 4 4
## Chain Moray Chalk Bass
## 4 4
## Cherubfish Chub (Bermuda/Yellow)
## 4 4
## Cleaning Goby Clown Wrasse
## 4 4
## Cocoa Damselfish Colon Goby
## 4 4
## Common Snook Coney
## 2 4
## Cottonwick Creole Wrasse
## 3 2
## Creole-fish Crevalle Jack
## 4 4
## Cubbyu Cubera Snapper
## 3 4
## Darkheaded Blenny Diamond Blenny
## 4 4
## Doctorfish Dog Snapper
## 3 4
## Dusky Damselfish Dusky Squirrelfish
## 3 3
## Eyed Flounder Fairy Basslet
## 2 3
## Flamefish Flying Gurnard
## 4 4
## Foureye Butterflyfish French Angelfish
## 4 3
## French Grunt Gag
## 4 4
## Glasseye Snapper Glassy Sweeper
## 4 1
## Goldentail Moray Goldspot Goby
## 2 2
## Goliath Grouper (Jewfish) Gray Angelfish
## 4 4
## Gray Snapper Gray Triggerfish
## 4 4
## Graysby Great Barracuda
## 2 2
## Greater Amberjack Greater Soapfish
## 4 2
## Green Moray Green Razorfish
## 3 2
## Green Sea Turtle Greenblotch Parrotfish
## 2 4
## Hairy Blenny Harlequin Bass
## 4 4
## Hawksbill Sea Turtle Highhat
## 4 3
## Hogfish Honeycomb Cowfish
## 4 4
## Horse-eye Jack Houndfish
## 4 4
## Hovering Goby Hybrid Hamlet
## 4 4
## Indigo Hamlet Jackknife Fish
## 3 3
## Jolthead Porgy Lancer Dragonet
## 3 3
## Lane Snapper Lantern Bass
## 3 2
## Lionfish Loggerhead Sea Turtle
## 2 4
## Longfin Damselfish Longjaw Squirrelfish
## 3 3
## Longsnout Butterflyfish Longspine Squirrelfish
## 3 3
## Mahogany Snapper Margate (Black)
## 3 2
## Margate (White) Masked/Glass Goby
## 3 4
## Midnight Parrotfish Molly Miller
## 4 4
## Mottled Mojarra Mutton Snapper
## 4 3
## Nassau Grouper Neon Goby
## 4 4
## Nurse Shark Ocean Surgeonfish
## 4 4
## Ocean Triggerfish Orangesided Goby
## 4 4
## Orangespotted Filefish Pallid Goby
## 2 4
## Palometa Peacock Flounder
## 4 3
## Pearl Blenny Pearly Razorfish
## 4 4
## Peppermint Bass Peppermint Goby
## 4 4
## Permit Pluma
## 4 2
## Porcupinefish Porkfish
## 2 4
## Princess Parrotfish Puddingwife
## 4 2
## Purple Reeffish Queen Angelfish
## 4 2
## Queen Parrotfish Queen Triggerfish
## 4 3
## Rainbow Parrotfish Rainbow Runner
## 2 4
## Rainbow Wrasse Red Grouper
## 4 3
## Red Hind Redband Parrotfish
## 2 3
## Redlip Blenny Redspotted Hawkfish
## 4 4
## Redtail Parrotfish Reef Croaker
## 2 4
## Reef Squirrelfish Reel Butterflyfish
## 3 2
## Rock Beauty Rock Hind
## 3 4
## Rosy Blenny Rosy Razorfish
## 4 4
## Roughhead Blenny Round Scad
## 4 4
## Rusty Goby Saddled Blenny
## 4 4
## Sailfin Blenny Sailors Choice
## 4 2
## Sand Diver Sand Perch
## 4 4
## Sand Tilefish Sargassum Triggerfish
## 2 4
## Saucereye Porgy Scamp
## 4 2
## Schoolmaster Scrawled Cowfish
## 2 3
## Scrawled Filefish Seaweed Blenny
## 4 4
## Secretary Blenny Sergeant Major
## 4 2
## Sharknose Goby Sharksucker
## 4 4
## Sharpnose Puffer Sharptail Eel
## 4 4
## Sheepshead Sheepshead Porgy
## 4 4
## Shortstripe Goby Shy Hamlet
## 3 2
## Silver Porgy Silversides
## 4 4
## Slender Filefish Slippery Dick
## 4 4
## Smallmouth Grunt Smooth Trunkfish
## 4 4
## Southern Sennet Southern Stingray
## 4 4
## Spanish Grunt Spanish Hogfish
## 4 2
## Spanish Mackerel Spiny Blenny
## 4 4
## Sponge Cardinalfish Spotfin Butterflyfish
## 4 3
## Spotfin Hogfish Spotlight Goby
## 3 4
## Spottail Pinfish Spotted Drum
## 4 4
## Spotted Eagle Ray Spotted Goatfish
## 2 4
## Spotted Moray Spotted Scorpionfish
## 4 4
## Spotted Trunkfish Squirrelfish
## 4 3
## Stoplight Parrotfish Striped Grunt
## 3 4
## Striped Parrotfish Sunshinefish
## 2 3
## Tan Hamlet Tarpon
## 4 4
## Threeline Basslet Threespot Damselfish
## 4 3
## Tiger Grouper Tobaccofish
## 2 4
## Tomtate Trumpetfish
## 4 4
## Twospot Cardinalfish Unidentified juvenile Grunt
## 4 4
## Unidentified Sea Turtle Unidentified Triplefin
## 4 4
## White Grunt Whitespotted Filefish
## 4 4
## Whitestar Cardinalfish Wrasse Bleny
## 4 4
## Yellow Goatfish Yellow Jack
## 4 4
## Yellow Stingray Yellowbelly Hamlet
## 4 4
## Yellowcheek Wrasse Yellowfin Grouper
## 4 4
## Yellowfin Mojarra Yellowhead Jawfish
## 4 2
## Yellowhead Wrasse Yellowline Goby
## 4 4
## Yellowmouth Grouper Yellownose Goby
## 2 4
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 4 3
## Yellowtail Damselfish Yellowtail Hamlet
## 4 4
## Yellowtail Reeffish Yellowtail Snapper
## 1 3
##
## Within cluster sum of squares by cluster:
## [1] 4.734627 5.010843 11.221328 2.758980
## (between_SS / total_SS = 95.2 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"## [1] 2 40 42 162## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.550 0.813 9.99 0.0900## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_12
## 1 0.8621329 -11.02288823 1.25092598 9 2
## 2 0.4481398 0.09035154 0.91433932 10 40
## 3 1.8956548 0.09035154 2.09120475 10 42
## 4 -0.6127615 0.09035154 0.05180039 10 162## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.0 10 4
## Arrow Blenny 0.0 10 4
## Atlantic Spadefish 0.0 10 4
## Balloonfish 0.1 10 4
## Banded Butterflyfish 0.6 10 2
## Bandtail Puffer 0.2 10 42014 K-Means
## K-means clustering with 4 clusters of sizes 1, 169, 36, 40
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 -0.6386303 -14.61611025
## 2 -0.5562018 0.10256919
## 3 2.1321229 -0.13106064
## 4 0.4470079 0.05000248
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 2 2
## Atlantic Spadefish Balloonfish
## 2 2
## Banded Butterflyfish Bandtail Puffer
## 3 2
## Bar Jack Barred Cardinalfish
## 3 2
## Barred Hamlet Beaugregory
## 2 2
## Belted Cardinalfish Belted Sandfish
## 2 2
## Bicolor Damselfish Black Durgon
## 3 3
## Black Grouper Black Hamlet
## 4 2
## Black Jack Blackbar Soldierfish
## 2 4
## Blackcap Basslet Blackear Wrasse
## 2 2
## Blackfin Snapper Blue Angelfish
## 2 2
## Blue Chromis Blue Goby
## 3 2
## Blue Hamlet Blue Parrotfish
## 2 2
## Blue Runner Blue Tang
## 2 3
## Bluehead Bluelip Parrotfish
## 3 2
## Bluespotted Cornetfish Bluestriped Grunt
## 2 3
## Boga Bonefish
## 2 2
## Bonnetmouth Bridled Goby
## 2 2
## Brown Chromis Brown Garden Eel
## 3 3
## Bucktooth Parrotfish Butter Hamlet
## 2 2
## Caesar Grunt Cero
## 2 2
## Chain Moray Chalk Bass
## 2 2
## Cherubfish Chub (Bermuda/Yellow)
## 2 4
## Cleaning Goby Clown Wrasse
## 3 2
## Cocoa Damselfish Colon Goby
## 3 2
## Common Snook Coney
## 2 4
## Cottonwick Creole Wrasse
## 2 4
## Creole-fish Crevalle Jack
## 2 2
## Cubbyu Cubera Snapper
## 2 2
## Darkheaded Blenny Diamond Blenny
## 2 2
## Doctorfish Dog Snapper
## 2 2
## Dusky Damselfish Dusky Squirrelfish
## 3 2
## Eyed Flounder Fairy Basslet
## 2 3
## Flamefish Flying Gurnard
## 4 2
## Foureye Butterflyfish French Angelfish
## 3 4
## French Grunt Gag
## 3 2
## Glasseye Snapper Glassy Sweeper
## 2 2
## Goldentail Moray Goldspot Goby
## 2 2
## Goliath Grouper (Jewfish) Gray Angelfish
## 2 4
## Gray Snapper Gray Triggerfish
## 2 2
## Graysby Great Barracuda
## 3 4
## Greater Amberjack Greater Soapfish
## 2 4
## Green Moray Green Razorfish
## 2 2
## Green Sea Turtle Greenblotch Parrotfish
## 2 2
## Hairy Blenny Harlequin Bass
## 2 4
## Hawksbill Sea Turtle Highhat
## 2 2
## Hogfish Honeycomb Cowfish
## 4 2
## Horse-eye Jack Houndfish
## 2 2
## Hovering Goby Hybrid Hamlet
## 2 2
## Indigo Hamlet Jackknife Fish
## 4 2
## Jolthead Porgy Lancer Dragonet
## 2 2
## Lane Snapper Lantern Bass
## 2 2
## Lionfish Loggerhead Sea Turtle
## 4 2
## Longfin Damselfish Longjaw Squirrelfish
## 3 2
## Longsnout Butterflyfish Longspine Squirrelfish
## 2 4
## Mahogany Snapper Margate (Black)
## 4 2
## Margate (White) Masked/Glass Goby
## 2 4
## Midnight Parrotfish Molly Miller
## 4 2
## Mottled Mojarra Mutton Snapper
## 2 4
## Nassau Grouper Neon Goby
## 4 2
## Nurse Shark Ocean Surgeonfish
## 2 3
## Ocean Triggerfish Orangesided Goby
## 2 2
## Orangespotted Filefish Pallid Goby
## 2 2
## Palometa Peacock Flounder
## 2 4
## Pearl Blenny Pearly Razorfish
## 2 2
## Peppermint Bass Peppermint Goby
## 2 2
## Permit Pluma
## 2 2
## Porcupinefish Porkfish
## 4 2
## Princess Parrotfish Puddingwife
## 3 2
## Purple Reeffish Queen Angelfish
## 2 4
## Queen Parrotfish Queen Triggerfish
## 3 2
## Rainbow Parrotfish Rainbow Runner
## 3 2
## Rainbow Wrasse Red Grouper
## 2 2
## Red Hind Redband Parrotfish
## 4 3
## Redlip Blenny Redspotted Hawkfish
## 2 2
## Redtail Parrotfish Reef Croaker
## 2 2
## Reef Squirrelfish Reel Butterflyfish
## 2 2
## Rock Beauty Rock Hind
## 3 4
## Rosy Blenny Rosy Razorfish
## 2 2
## Roughhead Blenny Round Scad
## 2 2
## Rusty Goby Saddled Blenny
## 2 2
## Sailfin Blenny Sailors Choice
## 2 2
## Sand Diver Sand Perch
## 2 2
## Sand Tilefish Sargassum Triggerfish
## 4 2
## Saucereye Porgy Scamp
## 2 2
## Schoolmaster Scrawled Cowfish
## 3 2
## Scrawled Filefish Seaweed Blenny
## 4 2
## Secretary Blenny Sergeant Major
## 2 3
## Sharknose Goby Sharksucker
## 2 2
## Sharpnose Puffer Sharptail Eel
## 3 2
## Sheepshead Sheepshead Porgy
## 2 2
## Shortstripe Goby Shy Hamlet
## 2 2
## Silver Porgy Silversides
## 2 1
## Slender Filefish Slippery Dick
## 2 3
## Smallmouth Grunt Smooth Trunkfish
## 2 4
## Southern Sennet Southern Stingray
## 2 2
## Spanish Grunt Spanish Hogfish
## 2 4
## Spanish Mackerel Spiny Blenny
## 2 2
## Sponge Cardinalfish Spotfin Butterflyfish
## 2 4
## Spotfin Hogfish Spotlight Goby
## 2 2
## Spottail Pinfish Spotted Drum
## 2 4
## Spotted Eagle Ray Spotted Goatfish
## 2 3
## Spotted Moray Spotted Scorpionfish
## 2 2
## Spotted Trunkfish Squirrelfish
## 4 3
## Stoplight Parrotfish Striped Grunt
## 3 2
## Striped Parrotfish Sunshinefish
## 4 2
## Tan Hamlet Tarpon
## 2 4
## Threeline Basslet Threespot Damselfish
## 2 3
## Tiger Grouper Tobaccofish
## 2 2
## Tomtate Trumpetfish
## 2 4
## Twospot Cardinalfish Unidentified juvenile Grunt
## 2 2
## Unidentified Sea Turtle Unidentified Triplefin
## 2 2
## White Grunt Whitespotted Filefish
## 4 4
## Whitestar Cardinalfish Wrasse Bleny
## 2 2
## Yellow Goatfish Yellow Jack
## 3 4
## Yellow Stingray Yellowbelly Hamlet
## 4 2
## Yellowcheek Wrasse Yellowfin Grouper
## 2 2
## Yellowfin Mojarra Yellowhead Jawfish
## 2 2
## Yellowhead Wrasse Yellowline Goby
## 3 2
## Yellowmouth Grouper Yellownose Goby
## 2 2
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 2 4
## Yellowtail Damselfish Yellowtail Hamlet
## 3 2
## Yellowtail Reeffish Yellowtail Snapper
## 2 3
##
## Within cluster sum of squares by cluster:
## [1] 0.000000 3.921278 36.422495 9.192672
## (between_SS / total_SS = 89.9 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"## [1] 1 169 36 40## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.507 0.794 9.95 0.476## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_14
## 1 -0.6386303 -14.61611025 6.968117e-09 3.000001 1
## 2 -0.5562018 0.10256919 6.548324e-02 10.000000 169
## 3 2.1321229 -0.13106064 2.201156e+00 9.888889 36
## 4 0.4470079 0.05000248 8.624584e-01 9.975000 40## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.000000 10 2
## Arrow Blenny 0.000000 10 2
## Atlantic Spadefish 0.000000 10 2
## Balloonfish 0.450000 10 2
## Banded Butterflyfish 2.119048 10 3
## Bandtail Puffer 0.000000 10 22016 K-Means
## K-means clustering with 4 clusters of sizes 3, 10, 20, 213
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 2.6275241 -8.981689
## 2 3.7641263 0.110885
## 3 1.3479576 0.110885
## 4 -0.3402957 0.110885
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 4 4
## Atlantic Spadefish Balloonfish
## 4 3
## Banded Butterflyfish Bandtail Puffer
## 2 4
## Bar Jack Barred Cardinalfish
## 4 4
## Barred Hamlet Beaugregory
## 4 4
## Belted Cardinalfish Belted Sandfish
## 4 4
## Bicolor Damselfish Black Durgon
## 3 2
## Black Grouper Black Hamlet
## 4 4
## Black Jack Blackbar Soldierfish
## 4 4
## Blackcap Basslet Blackear Wrasse
## 4 4
## Blackfin Snapper Blue Angelfish
## 4 4
## Blue Chromis Blue Goby
## 2 4
## Blue Hamlet Blue Parrotfish
## 4 4
## Blue Runner Blue Tang
## 4 1
## Bluehead Bluelip Parrotfish
## 2 4
## Bluespotted Cornetfish Bluestriped Grunt
## 4 4
## Boga Bonefish
## 4 4
## Bonnetmouth Bridled Goby
## 4 4
## Brown Chromis Brown Garden Eel
## 4 1
## Bucktooth Parrotfish Butter Hamlet
## 4 4
## Caesar Grunt Cero
## 4 4
## Chain Moray Chalk Bass
## 4 4
## Cherubfish Chub (Bermuda/Yellow)
## 4 4
## Cleaning Goby Clown Wrasse
## 3 4
## Cocoa Damselfish Colon Goby
## 4 4
## Common Snook Coney
## 4 4
## Cottonwick Creole Wrasse
## 4 4
## Creole-fish Crevalle Jack
## 4 4
## Cubbyu Cubera Snapper
## 4 4
## Darkheaded Blenny Diamond Blenny
## 4 4
## Doctorfish Dog Snapper
## 4 4
## Dusky Damselfish Dusky Squirrelfish
## 3 4
## Eyed Flounder Fairy Basslet
## 4 2
## Flamefish Flying Gurnard
## 4 4
## Foureye Butterflyfish French Angelfish
## 2 3
## French Grunt Gag
## 2 4
## Glasseye Snapper Glassy Sweeper
## 4 4
## Goldentail Moray Goldspot Goby
## 4 4
## Goliath Grouper (Jewfish) Gray Angelfish
## 4 4
## Gray Snapper Gray Triggerfish
## 4 4
## Graysby Great Barracuda
## 4 4
## Greater Amberjack Greater Soapfish
## 4 3
## Green Moray Green Razorfish
## 4 4
## Green Sea Turtle Greenblotch Parrotfish
## 4 4
## Hairy Blenny Harlequin Bass
## 4 4
## Hawksbill Sea Turtle Highhat
## 4 4
## Hogfish Honeycomb Cowfish
## 3 4
## Horse-eye Jack Houndfish
## 4 4
## Hovering Goby Hybrid Hamlet
## 4 4
## Indigo Hamlet Jackknife Fish
## 4 4
## Jolthead Porgy Lancer Dragonet
## 4 4
## Lane Snapper Lantern Bass
## 4 4
## Lionfish Loggerhead Sea Turtle
## 3 4
## Longfin Damselfish Longjaw Squirrelfish
## 4 4
## Longsnout Butterflyfish Longspine Squirrelfish
## 4 4
## Mahogany Snapper Margate (Black)
## 4 4
## Margate (White) Masked/Glass Goby
## 4 4
## Midnight Parrotfish Molly Miller
## 3 4
## Mottled Mojarra Mutton Snapper
## 4 3
## Nassau Grouper Neon Goby
## 4 4
## Nurse Shark Ocean Surgeonfish
## 4 4
## Ocean Triggerfish Orangesided Goby
## 4 4
## Orangespotted Filefish Pallid Goby
## 4 4
## Palometa Peacock Flounder
## 4 4
## Pearl Blenny Pearly Razorfish
## 4 4
## Peppermint Bass Peppermint Goby
## 4 4
## Permit Pluma
## 4 4
## Porcupinefish Porkfish
## 4 4
## Princess Parrotfish Puddingwife
## 2 4
## Purple Reeffish Queen Angelfish
## 4 3
## Queen Parrotfish Queen Triggerfish
## 4 4
## Rainbow Parrotfish Rainbow Runner
## 4 4
## Rainbow Wrasse Red Grouper
## 4 4
## Red Hind Redband Parrotfish
## 3 4
## Redlip Blenny Redspotted Hawkfish
## 4 4
## Redtail Parrotfish Reef Croaker
## 4 4
## Reef Squirrelfish Reel Butterflyfish
## 4 4
## Rock Beauty Rock Hind
## 3 4
## Rosy Blenny Rosy Razorfish
## 4 4
## Roughhead Blenny Round Scad
## 4 4
## Rusty Goby Saddled Blenny
## 4 4
## Sailfin Blenny Sailors Choice
## 4 4
## Sand Diver Sand Perch
## 4 4
## Sand Tilefish Sargassum Triggerfish
## 4 4
## Saucereye Porgy Scamp
## 4 4
## Schoolmaster Scrawled Cowfish
## 3 4
## Scrawled Filefish Seaweed Blenny
## 3 4
## Secretary Blenny Sergeant Major
## 4 1
## Sharknose Goby Sharksucker
## 4 4
## Sharpnose Puffer Sharptail Eel
## 4 4
## Sheepshead Sheepshead Porgy
## 4 4
## Shortstripe Goby Shy Hamlet
## 4 4
## Silver Porgy Silversides
## 4 4
## Slender Filefish Slippery Dick
## 4 4
## Smallmouth Grunt Smooth Trunkfish
## 4 3
## Southern Sennet Southern Stingray
## 4 4
## Spanish Grunt Spanish Hogfish
## 4 3
## Spanish Mackerel Spiny Blenny
## 4 4
## Sponge Cardinalfish Spotfin Butterflyfish
## 4 3
## Spotfin Hogfish Spotlight Goby
## 4 4
## Spottail Pinfish Spotted Drum
## 4 4
## Spotted Eagle Ray Spotted Goatfish
## 4 4
## Spotted Moray Spotted Scorpionfish
## 4 4
## Spotted Trunkfish Squirrelfish
## 4 2
## Stoplight Parrotfish Striped Grunt
## 2 4
## Striped Parrotfish Sunshinefish
## 4 4
## Tan Hamlet Tarpon
## 4 3
## Threeline Basslet Threespot Damselfish
## 4 4
## Tiger Grouper Tobaccofish
## 4 4
## Tomtate Trumpetfish
## 4 4
## Twospot Cardinalfish Unidentified juvenile Grunt
## 4 4
## Unidentified Sea Turtle Unidentified Triplefin
## 4 4
## White Grunt Whitespotted Filefish
## 4 4
## Whitestar Cardinalfish Wrasse Bleny
## 4 4
## Yellow Goatfish Yellow Jack
## 4 4
## Yellow Stingray Yellowbelly Hamlet
## 4 4
## Yellowcheek Wrasse Yellowfin Grouper
## 4 4
## Yellowfin Mojarra Yellowhead Jawfish
## 4 4
## Yellowhead Wrasse Yellowline Goby
## 4 4
## Yellowmouth Grouper Yellownose Goby
## 4 4
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 4 4
## Yellowtail Damselfish Yellowtail Hamlet
## 3 4
## Yellowtail Reeffish Yellowtail Snapper
## 4 4
##
## Within cluster sum of squares by cluster:
## [1] 6.775944 4.386883 5.016937 5.416670
## (between_SS / total_SS = 95.6 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"## [1] 3 10 20 213## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.193 0.491 9.99 0.110## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_16
## 1 2.6275241 -8.981689 1.4839505 9 3
## 2 3.7641263 0.110885 2.0423332 10 10
## 3 1.3479576 0.110885 0.8553333 10 20
## 4 -0.3402957 0.110885 0.0259390 10 213## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.0000000 10 4
## Arrow Blenny 0.0000000 10 4
## Atlantic Spadefish 0.0000000 10 4
## Balloonfish 0.8333333 10 3
## Banded Butterflyfish 1.8500000 10 2
## Bandtail Puffer 0.0000000 10 42018 K-Means
## K-means clustering with 4 clusters of sizes 53, 117, 72, 4
##
## Cluster means:
## MEAN_YEARLY_DI N_Sites
## 1 1.5649029 0.02820007
## 2 -0.8156263 0.12886692
## 3 0.1110118 0.12455030
## 4 1.1238945 -6.38491389
##
## Clustering vector:
## Almaco Jack Arrow Blenny
## 2 2
## Atlantic Spadefish Balloonfish
## 2 3
## Banded Butterflyfish Bandtail Puffer
## 1 3
## Bar Jack Barred Cardinalfish
## 1 2
## Barred Hamlet Beaugregory
## 3 1
## Belted Cardinalfish Belted Sandfish
## 2 2
## Bicolor Damselfish Black Durgon
## 1 1
## Black Grouper Black Hamlet
## 3 3
## Black Jack Blackbar Soldierfish
## 2 3
## Blackcap Basslet Blackear Wrasse
## 1 2
## Blackfin Snapper Blue Angelfish
## 2 3
## Blue Chromis Blue Goby
## 1 2
## Blue Hamlet Blue Parrotfish
## 3 3
## Blue Runner Blue Tang
## 2 1
## Bluehead Bluelip Parrotfish
## 1 2
## Bluespotted Cornetfish Bluestriped Grunt
## 2 1
## Boga Bonefish
## 3 2
## Bonnetmouth Bridled Goby
## 2 2
## Brown Chromis Brown Garden Eel
## 1 4
## Bucktooth Parrotfish Butter Hamlet
## 2 2
## Caesar Grunt Cero
## 3 2
## Chain Moray Chalk Bass
## 2 2
## Cherubfish Chub (Bermuda/Yellow)
## 3 1
## Cleaning Goby Clown Wrasse
## 1 2
## Cocoa Damselfish Colon Goby
## 1 3
## Common Snook Coney
## 2 3
## Cottonwick Creole Wrasse
## 2 3
## Creole-fish Crevalle Jack
## 2 2
## Cubbyu Cubera Snapper
## 2 2
## Darkheaded Blenny Diamond Blenny
## 2 1
## Doctorfish Dog Snapper
## 1 3
## Dusky Damselfish Dusky Squirrelfish
## 1 1
## Eyed Flounder Fairy Basslet
## 2 1
## Flamefish Flying Gurnard
## 2 2
## Foureye Butterflyfish French Angelfish
## 1 1
## French Grunt Gag
## 1 2
## Glasseye Snapper Glassy Sweeper
## 2 2
## Goldentail Moray Goldspot Goby
## 2 1
## Goliath Grouper (Jewfish) Gray Angelfish
## 2 3
## Gray Snapper Gray Triggerfish
## 3 2
## Graysby Great Barracuda
## 1 3
## Greater Amberjack Greater Soapfish
## 2 3
## Green Moray Green Razorfish
## 3 2
## Green Sea Turtle Greenblotch Parrotfish
## 3 3
## Hairy Blenny Harlequin Bass
## 2 3
## Hawksbill Sea Turtle Highhat
## 2 2
## Hogfish Honeycomb Cowfish
## 3 3
## Horse-eye Jack Houndfish
## 1 2
## Hovering Goby Hybrid Hamlet
## 2 2
## Indigo Hamlet Jackknife Fish
## 1 2
## Jolthead Porgy Lancer Dragonet
## 3 2
## Lane Snapper Lantern Bass
## 3 2
## Lionfish Loggerhead Sea Turtle
## 3 2
## Longfin Damselfish Longjaw Squirrelfish
## 1 1
## Longsnout Butterflyfish Longspine Squirrelfish
## 3 4
## Mahogany Snapper Margate (Black)
## 3 2
## Margate (White) Masked/Glass Goby
## 3 3
## Midnight Parrotfish Molly Miller
## 1 3
## Mottled Mojarra Mutton Snapper
## 2 1
## Nassau Grouper Neon Goby
## 3 3
## Nurse Shark Ocean Surgeonfish
## 3 1
## Ocean Triggerfish Orangesided Goby
## 3 2
## Orangespotted Filefish Pallid Goby
## 3 2
## Palometa Peacock Flounder
## 2 3
## Pearl Blenny Pearly Razorfish
## 2 2
## Peppermint Bass Peppermint Goby
## 2 2
## Permit Pluma
## 2 2
## Porcupinefish Porkfish
## 3 2
## Princess Parrotfish Puddingwife
## 1 2
## Purple Reeffish Queen Angelfish
## 3 1
## Queen Parrotfish Queen Triggerfish
## 3 3
## Rainbow Parrotfish Rainbow Runner
## 3 3
## Rainbow Wrasse Red Grouper
## 2 2
## Red Hind Redband Parrotfish
## 1 1
## Redlip Blenny Redspotted Hawkfish
## 3 2
## Redtail Parrotfish Reef Croaker
## 1 2
## Reef Squirrelfish Reel Butterflyfish
## 4 1
## Rock Beauty Rock Hind
## 1 3
## Rosy Blenny Rosy Razorfish
## 2 2
## Roughhead Blenny Round Scad
## 2 2
## Rusty Goby Saddled Blenny
## 2 3
## Sailfin Blenny Sailors Choice
## 2 2
## Sand Diver Sand Perch
## 3 2
## Sand Tilefish Sargassum Triggerfish
## 3 2
## Saucereye Porgy Scamp
## 3 2
## Schoolmaster Scrawled Cowfish
## 1 2
## Scrawled Filefish Seaweed Blenny
## 3 2
## Secretary Blenny Sergeant Major
## 2 1
## Sharknose Goby Sharksucker
## 2 2
## Sharpnose Puffer Sharptail Eel
## 1 2
## Sheepshead Sheepshead Porgy
## 2 3
## Shortstripe Goby Shy Hamlet
## 2 2
## Silver Porgy Silversides
## 2 2
## Slender Filefish Slippery Dick
## 2 2
## Smallmouth Grunt Smooth Trunkfish
## 3 1
## Southern Sennet Southern Stingray
## 2 3
## Spanish Grunt Spanish Hogfish
## 2 1
## Spanish Mackerel Spiny Blenny
## 2 2
## Sponge Cardinalfish Spotfin Butterflyfish
## 2 1
## Spotfin Hogfish Spotlight Goby
## 2 2
## Spottail Pinfish Spotted Drum
## 2 3
## Spotted Eagle Ray Spotted Goatfish
## 2 3
## Spotted Moray Spotted Scorpionfish
## 2 2
## Spotted Trunkfish Squirrelfish
## 3 1
## Stoplight Parrotfish Striped Grunt
## 1 3
## Striped Parrotfish Sunshinefish
## 1 3
## Tan Hamlet Tarpon
## 2 1
## Threeline Basslet Threespot Damselfish
## 2 1
## Tiger Grouper Tobaccofish
## 3 2
## Tomtate Trumpetfish
## 2 3
## Twospot Cardinalfish Unidentified juvenile Grunt
## 2 3
## Unidentified Sea Turtle Unidentified Triplefin
## 2 2
## White Grunt Whitespotted Filefish
## 3 3
## Whitestar Cardinalfish Wrasse Bleny
## 2 2
## Yellow Goatfish Yellow Jack
## 1 3
## Yellow Stingray Yellowbelly Hamlet
## 3 2
## Yellowcheek Wrasse Yellowfin Grouper
## 2 2
## Yellowfin Mojarra Yellowhead Jawfish
## 3 2
## Yellowhead Wrasse Yellowline Goby
## 1 4
## Yellowmouth Grouper Yellownose Goby
## 2 3
## Yellowprow Goby Yellowtail (Redfin)Parrotfish
## 2 3
## Yellowtail Damselfish Yellowtail Hamlet
## 1 3
## Yellowtail Reeffish Yellowtail Snapper
## 2 1
##
## Within cluster sum of squares by cluster:
## [1] 31.56526 16.01667 15.58508 47.09595
## (between_SS / total_SS = 77.5 %)
##
## Available components:
##
## [1] "cluster" "centers" "totss" "withinss" "tot.withinss"
## [6] "betweenss" "size" "iter" "ifault"## [1] 53 117 72 4## # A tibble: 1 x 4
## MEAN_DI SD_DI MEAN_SITES SD_SITES
## <dbl> <dbl> <dbl> <dbl>
## 1 0.833 0.838 9.91 0.495## MEAN_YEARLY_DI N_Sites DI_CENTERS SITES_CENTERS CLUSTER_SIZE_18
## 1 1.5649029 0.02820007 2.1440958 9.924528 53
## 2 -0.8156263 0.12886692 0.1493352 9.974359 117
## 3 0.1110118 0.12455030 0.9258102 9.972222 72
## 4 1.1238945 -6.38491389 1.7745536 6.750000 4## MEAN_YEARLY_DI N_Sites cluster
## Almaco Jack 0.300000 10 2
## Arrow Blenny 0.100000 10 2
## Atlantic Spadefish 0.400000 10 2
## Balloonfish 1.500000 10 3
## Banded Butterflyfish 2.103571 10 1
## Bandtail Puffer 0.700000 10 3Visualize Yearly Clusters
